Factors Structuring Microbial Communities in Highl

TYPE Original Research
PUBLISHED 07 September 2022

DOI 10.3389/fmicb.2022.937683
Factors structuring microbial

OPEN ACCESS communities in highly impacted
EDITED BY
Danny Ionescu,
Leibniz-Institute of Freshwater Ecology
coastal marine sediments (Mar
and Inland Fisheries (IGB), Germany
REVIEWED BY
Menor lagoon, SE Spain)
Gustavo Bueno Gregoracci,
Federal University of São Paulo, Brazil
Carmen Rizzo, Borja Aldeguer-Riquelme1 , Esther Rubio-Portillo1 ,
Stazione Zoologica Anton Dohrn José Álvarez-Rogel2 , Francisca Giménez-Casalduero3 ,
Napoli, Italy
*CORRESPONDENCE
Xose Luis Otero4 , María-Dolores Belando5 ,
Josefa Antón Jaime Bernardeau-Esteller5 , Rocío García-Muñoz5 ,
[email protected]
Aitor Forcada3 , Juan M. Ruiz5 , Fernando Santos1 and
SPECIALTY SECTION
This article was submitted to Josefa Antón1,6*
Aquatic Microbiology,
1
a section of the journal Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain,
2
Frontiers in Microbiology Department of Agricultural Engineering of the Escuela Técnica Superior Ingeniería Agronómica
(ETSIA) & Soil Ecology and Biotechnology Unit of the Institute of Plant Biotechnology, Technical
RECEIVED 06 May 2022 University of Cartagena, Cartagena, Spain, 3 Department of Marine Science and Applied Biology,
ACCEPTED 27 July 2022 University of Alicante, Alicante, Spain, 4 Cross-Research in Environmental Technologies (CRETUS),
PUBLISHED 07 September 2022 Departamento de Edafoloxía e Química Agrícola, Facultade de Bioloxía, Universidade de Santiago
CITATION
de Compostela, Santiago de Compostela, Spain, 5 Seagrass Ecology Group, Spanish Oceanography
Aldeguer-Riquelme B, Rubio-Portillo E, Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain,
6
Álvarez-Rogel J, Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante,
Giménez-Casalduero F, Otero XL, Alicante, Spain
Belando M-D, Bernardeau-Esteller J,
García-Muñoz R, Forcada A, Ruiz JM,
Santos F and Antón J (2022) Factors
structuring microbial communities
in highly impacted coastal marine Coastal marine lagoons are environments highly vulnerable to anthropogenic
sediments (Mar Menor lagoon, SE pressures such as agriculture nutrient loading or runoff from metalliferous
Spain).
Front. Microbiol. 13:937683. mining. Sediment microorganisms, which are key components in the
doi: 10.3389/fmicb.2022.937683 biogeochemical cycles, can help attenuate these impacts by accumulating
COPYRIGHT nutrients and pollutants. The Mar Menor, located in the southeast of
© 2022 Aldeguer-Riquelme, Spain, is an example of a coastal lagoon strongly altered by anthropic
Rubio-Portillo, Álvarez-Rogel,
Giménez-Casalduero, Otero, Belando, pressures, but the microbial community inhabiting its sediments remains
Bernardeau-Esteller, García-Muñoz, unknown. Here, we describe the sediment prokaryotic communities along
Forcada, Ruiz, Santos and Antón. This
is an open-access article distributed a wide range of environmental conditions in the lagoon, revealing that
under the terms of the Creative microbial communities were highly heterogeneous among stations, although
Commons Attribution License (CC BY).
The use, distribution or reproduction in
a core microbiome was detected. The microbiota was dominated by
other forums is permitted, provided Delta- and Gammaproteobacteria and members of the Bacteroidia class.
the original author(s) and the copyright
Additionally, several uncultured groups such as Asgardarchaeota were
owner(s) are credited and that the
original publication in this journal is detected in relatively high proportions. Sediment texture, the presence
cited, in accordance with accepted of Caulerpa or Cymodocea, depth, and geographic location were among
academic practice. No use, distribution
or reproduction is permitted which the most important factors structuring microbial assemblages. Furthermore,
does not comply with these terms. microbial communities in the stations with the highest concentrations
of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable
Frontiers in Microbiology 01 frontiersin.org

Aldeguer-Riquelme et al. 10.3389/fmicb.2022.937683
than those in the non-contaminated stations. This finding suggests that

bacteria colonizing heavily contaminated stations are specialists sensitive
to change.
KEYWORDS
16S rRNA gene amplicon sequencing, coastal lagoon, Mar Menor, sediment, microbial
community
Introduction by several anthropogenic factors (Marín-Guirao et al., 2005;

Conesa and Jiménez-Cárceles, 2007; León et al., 2013, 2017,
Coastal lagoons are highly biodiverse and productive 2018; Jiménez-Martinez et al., 2016; Romero et al., 2020).
environments that provide critical ecosystem services with In the 1970s, one inlet (El Estacio channel) connecting the
significant socioeconomic impacts such as food provision or lagoon with the Mediterranean Sea was broadened (Mas, 1994),
climate regulation (Newton et al., 2018). They are shallow water drastically changing the hydrodynamic regime and decreasing
bodies separated from the ocean by a barrier and connected the lagoon temperature and salinity toward the values closer
to it by one or more restricted inlets (Kjerfve, 1994). Due to to those typically measured in the adjacent Mediterranean Sea
their proximity to land, small volumes, and long water renewal (37 psu). This event, together with the massive loading of urban
time, coastal lagoons are extremely sensitive to anthropic sewage into the lagoon, allowed the spread of the opportunistic
eutrophication and pollutant accumulation, such as agricultural chlorophyte Caulerpa prolifera (Ballester, 1985; Terrados and
nutrient loading, fishing, tourism, and mining (Barbier et al., Ros, 1992). Furthermore, due to the past extractive activity
2011; Pérez-Ruzafa and Marcos, 2012), which may promote in the Cartagena-La Unión mining district, located close to
sudden and drastic changes in ecosystem structure, functions, the southern basin (Conesa and Schulin, 2010), PTEs such
and services (De Wit et al., 2001). as Pb, Zn, Cd, and As have been loaded into the lagoon by
Sediments are a key compartment for the functioning and hydric and aeolian erosion and surface and subsurface runoffs.
quality of coastal lagoons by acting as a sink for organic matter These PTEs accumulate in the sediment (Simonneau, 1973;
(Hewson and Fuhrman, 2008), potentially toxic elements (PTEs) García and Muñoz-Vera, 2015) or are taken up by vegetation
(i.e., metals and metalloids), and inorganic nutrients such as and fauna (Serrano et al., 2019; Romero et al., 2020). In
N or P (Jiménez-Cárceles et al., 2006; Sharifuzzaman et al., addition, the increase in tourism activity since the 1960s,
2016). Conversely, sediments can transfer nutrients and PTEs and the effects of intensive agriculture since the 1970s, have
into the water column by diffusion or when sediment particles deeply transformed the surrounding territory and poured huge
are suspended by winds and currents. Due to the presence of a amounts of sediments, nutrients, and contaminants into the
high nutrient load in sediments, resident microbial communities lagoon (Jiménez-Martinez et al., 2016; Pérez-Ruzafa et al., 2019).
are usually very dense, reaching up to 109 cells/g (Luna et al., These impacts have shifted the lagoon from an oligotrophic
2002; Petro et al., 2019), which is 3-4 orders of magnitude higher system dominated by the seagrass Cymodocea nodosa (Ballester,
than microbial densities in the water column (DeLong et al., 1985), to an eutrophic system that caused the macroalga
1999; Eilers et al., 2000). Furthermore, diffusion of O2 through C. prolifera to rapidly colonize, forming monospecific or mixed
the sediment is limited (Hewson and Fuhrman, 2008), which meadows with C. nodosa (Ballester, 1985; Terrados and Ros,
leads to redox zoning and changes in microbial metabolism. At 1991) (hereafter we will refer to these species as Caulerpa and
the surface, organic matter is oxidized by aerobic microbes that Cymodocea, respectively). Contaminants of emerging concern,
deplete available O2 ; in deeper layers, anaerobes use alternative such as pesticides, polycyclic aromatic hydrocarbons (PAHs),
electron acceptors such as NO3 − , MnO2 , amorphous FeOOH, surfactants, and pharmaceuticals, have also been detected in
and SO4 2− (Sørensen et al., 1979). Due to their high abundances the lagoon-associated watercourses, water columns, sediments,
and metabolic diversity, microorganisms in marine sediments and even in bivalves and fishes (Moreno-González et al.,
are a key factor in the remineralization of nutrients (Alongi, 2014, 2016; Jiménez-Martinez et al., 2016). Furthermore, the
1994, 1998); and thus, they have a strong influence on the lagoon experienced a unique and severe event of the so-
biogeochemical cycles of coastal marine ecosystems. called “ecosystem disruptive algal bloom” as a consequence
The Mar Menor, located in the southeast of Spain (Figure 1), of a phytoplankton overgrowth initiated in 2016 by the
is the largest hypersaline (i.e., 42–47 psu) coastal lagoon in cyanobacterium Synechoccocus (Aguilar-Escribano et al., 2016;
Europe and provides a paradigmatic example of a coastal Mercado et al., 2021). This caused the water turbidity to increase
marine ecosystem that is highly valuable yet strongly altered up to critical levels for macrophyte survival and led to the

FIGURE 1
Geographic location and sampling stations in the Mar Menor lagoon. Levels of different factors (depth, vegetation, and texture) are indicated by
symbols (see legend at the right) for each sampling site. The symbols colored in gray indicate stations selected for microbiological studies.
sudden loss of 82% of benthic vegetation, including Caulerpa Mining activity-derived PTEs, which were present in extremely
and Cymodocea (Belando-Torrente et al., 2019; Marín-Guirao high concentrations in the south of the lagoon, also affected
et al., 2019). prokaryotic composition and stability, indicating the capacity of
Some studies have addressed the effects of these anthropic sustained human pressures to alter sediment microbiomes and,
impacts on the macro-organisms inhabiting the lagoon (Muñoz- likely, their ecosystem functions.
Vera et al., 2015; Serrano et al., 2019; Romero et al., 2020) and
on benthic food webs (Marín-Guirao et al., 2008). However, the
information available on the microbial ecology of the system Materials and methods
is very scarce and restricted to the water column (Gilabert,
2001; Ghai et al., 2012). Thus, despite the ecological relevance Study area
of sediment microbiota in coastal lagoons, to date, nothing
is known about this component of the microbial assemblage The Mar Menor is a hypersaline shallow coastal lagoon
in the Mar Menor. To fill this gap, we aimed at ascertaining (maximum depth 7 m and average depth 4.5 m) located in
whether (i) the taxonomic composition and inferred putative the Region of Murcia, southeast of Spain, with an area of
metabolic capabilities of the Mar Menor sediments were similar 135 km2 . It is separated from the Mediterranean Sea by a sand
to that of other marine sediments, (ii) factors such as texture, bar of 22 km length (Figure 1) and connected to it by three
depth, vegetation, and geographical location could be linked small inlets through which water exchanges between both water
to the microbial community structure, and (iii) microbial bodies occur. The Mar Menor water mass is then relatively
communities in each station underwent temporal changes. confined with a renewal time of about 1 year (Fraile-Nuez et al.,
Our results showed that the microbial communities in the 2018) and has a salinity range of 42–47 psu (Aravio-Torre and
analyzed sediments were highly heterogeneous among stations, Arévalo, 1973), higher than that of the adjacent Mediterranean
although a core microbiome could be detected. Sediment Sea in this area (37–38.5 psu; Pérez-Ruzafa et al., 2004). Water
texture, vegetation type, depth, and geographical location were temperature varies from 10◦ C in winter to 31◦ C in summer,
found to drive the structure of the microbial community, while without a significant stratification in the water column (Fraile-
time was only relevant in the most PTE contaminated stations. Nuez et al., 2018). Nitrate concentrations were below 1 µM

until the 1990s when agricultural and urban wastes increased according to Vepraskas and Faulkner (Vepraskas and Faulkner,
the concentration above 8 µM (Ruiz et al., 2020). Curiously, 2001), by adding +200 mV to the measured voltage (the value
chlorophyll concentrations did not significantly increase above of the Ag/AgCl reference electrode at 20◦ C). Then, sediment
1–3 mg/m3 until 2016, when the macrophyte populations in the interstitial water was extracted by centrifugation at 11,300 g in
Mar Menor lagoon collapsed due to a massive phytoplankton a refrigerated centrifuge at 4◦ C under a nitrogen atmosphere.
bloom (Belando-Torrente et al., 2019; Pérez-Ruzafa et al., 2019; The dissolved sulfide was immediately measured (Cline, 1969).
Ruiz et al., 2020). The rest of the interstitial water samples were stored at 4◦ C to
measure electrical conductivity (EC), dissolved organic carbon
(DOC), NO3 − and NH4 + within less than 1 week after the
Field sampling sampling. The DOC was measured in a TOC-automatic analyzer
(TOC-VCSH Shimadzu). The NO3 − and NH4 + concentrations
A total of 22 sampling stations were distributed across were measured with a V/UV spectrometer at λ = 220 nm and at
the lagoon (Figure 1) based on depth (<2, 2–4, and >4 m), λ = 670 nm, respectively, and the interference by organic matter
sediment texture (sandy and muddy), and vegetation (bared, was corrected by measuring the absorbance at λ = 275 nm
Caulerpa and Cymodocea) according to the information (AOAC, 1975; Neiker, 2005). The solid material was dried at
from previous studies (bathymetry from MAGRAMA, 2008; room temperature. Each dried sample was passed through a
sediment characteristics from Álvarez-Rogel et al., 2019; 2-mm mesh and a fraction larger than this size (mainly large
macrophytes distribution from Belando et al., 2021). At each mollusk shells) was discarded. The particle size was assessed
sampling point, in March and September of 2018, cold and with the 2-mm sieved aliquots, which were put in an ultrasonic
warm season, respectively, and both characterized to be dry bath for 10 min to promote particle dispersion. Then, they were
seasons in this area, a lineal transect of 25 m was fixed, sieved to 50 µm under a stream of water. Both fractions (sand,
depth and presence of vegetation was validated in situ by from 2 mm to 50 µm; silt + clay, <50 µm) were dried and
divers, and sediment samples were collected using cores (7- weighed and the percentage of each one was calculated. Aliquots
cm diameter) along the transect area as follows. Three surface of the 2-mm sieved samples were crushed in an agate mortar for
sediment samples (4.5 cm) were collected for microbial analysis measuring total element concentrations (X-ray fluorescence).
using cores (7 cm diameter) that were distributed at the The amorphous or poorly crystalline Fe oxyhydroxides (FeA)
beginning, center, and end of each transect. For physicochemical were extracted by shaking 2-mm sieved samples for 6 h
determination, five replicates per sampling point, collected at 96◦ C with 30 ml 0.04 M hydroxylamine + 25% acetic
every 5 m of the line transect, were homogenized prior to the acid (v/v) (Fortin et al., 1993). The degree of Fe pyritization
analyses. The samples were not split by the depth due to the (DOP) was calculated to establish the percentage of reactive
heterogeneous vertical profiles of physicochemical parameters iron incorporated into the pyrite fraction. The calculation was
in the first 4 cm among the samples from different stations, made using Eq. 1, assuming reactive-Fe to be extracted with
which hampered the definition of a vertical common cutoff dithionite (DOP-dithionite), according to the recommendations
for the oxic–anoxic boundary. The samples were taken to the of Raiswell et al. (1994).
laboratory in a portable 4◦ C cooler.
Pyrite Fe
For microbial analyses, the individual sediment samples DOP (%) = × 100 (1)
Pyrite Fe + Reactive Fe
were weighted and manually homogenized after adding 50 ml
of 1X PBS containing 3.5% NaCl. Then, for cell density The concentration of acid volatile sulfides (AVS = 6FeS,
measurements, 1 ml of each sample was fixed with formaldehyde Fe3 S4 , H2 S) was determined in triplicate using 0.5–1.0 g of
(4% final concentration, 4 h at 4◦ C) and the fixation stopped wet sample, according to the method described by Kostka and
with 9 ml of 1X PBS. Cell counts in each station were determined Luther (1994). Sulfide from AVS was liberated with 20 ml
by epifluorescence microscopy after DAPI staining (Gomariz 3N HCl previously deaerated for 40–50 min. The sample was
et al., 2015). The remaining homogenized sediments were stored digested in a gas-tight reaction flask for 40–50 min under a
at –80◦ C until processed for nucleic acid extraction (see below). continuous flow of nitrogen, which was bubbled through the
flask as slowly as possible. The evolved H2 S was then received in
a trap containing 25 ml of 3% Zn acetate, 1 ml of concentrated
Physicochemical measurements H2 SO4 , and 4 ml of diamine reagent, and precipitated as
ZnS. Sulfide was then measured colorimetrically with a UV-
Sediments for physicochemical analysis were processed VIS spectrophotometer at a wavelength of 670 nm using the
immediately upon arrival at the laboratory. The redox potential methylene blue method of Cline (Cline, 1969). Metal(loid)s
(Eh) and pH values were measured three times per homogenized simultaneously extracted with AVS (SEM-AVS), which is an
sample by inserting Eh and pH electrodes (Crison 50–55 approach to assess the potential for metal ions found in sediment
and Crison 50–50, respectively). The Eh values were adjusted, to cause toxic effects in sediment-dwelling organisms, were

analyzed by ICP-OES (Perkin Elmer, Optima model 4300 DV, vegan package (Oksanen, 2011) with the parameter “range.”
Sunny vale, CA, United States) in 3N HCl. Correlations among the environmental variables were assessed
by the function “cor” and variables with correlations coefficients
above 0.85 were considered correlated.
DNA extraction, 16S rRNA gene PCR Rarefactions curves were generated in R with the rarecurve
amplification, and sequencing function of the “vegan” package. The α-diversity measures
(Shannon index and observed OTUs) were calculated with
Based on a 3D PCA with the physicochemical characteristics the “estimate_richness” function of the “phyloseq” package
(Supplementary Figure 1), fourteen stations (corresponding to (McMurdie and Holmes, 2013). In addition, unique and
82 samples, including triplicates per station and sampling time, shared OTUs among samples were displayed with the
except P8 with duplicates) were selected as representative of all “UpSet” (visualizing intersecting sets) diagram using the “R-
the physicochemical and environmental conditions in the Mar bioconductor” package “UpSetR” (Conway et al., 2017). For this
Menor sediments and were analyzed microbiologically. analysis, we only considered OTUs above 0.1% in each sample
To extract DNA, the RNeasy Power Soil Total RNA Kit which could be considered an abundant biosphere given the
(Qiagen) and its complementary RNeasy Power Soil DNA high diversity of these samples.
Elution Kit (Qiagen) were used. Two grams of the homogenized An analysis of variance (ANOVA) was used to test
sediment samples, stored at –80◦ C, were used according to the for statistical differences in physicochemical variables,
manufacturer’s instructions. QubitTM dsDNA High Sensitivity concentration of cells, observed OTUs, Shannon index,
(HS) or Broad Range (BR) (Invitrogen) kits were employed to and relative abundance of detected microbial classes among
measure DNA concentration. the levels of each of the following factors considered: Texture
The 82 extracted DNAs were used for PCR amplification (levels: mud and sand), time (levels: March and September),
of the 16S rRNA genes V3-V4 regions, using 25 cycles and vegetation (levels: bared, Caulerpa and Cymodocea), depth
primers 341F–805R (Takahashi et al., 2014). The PCR products (levels: shallow, intermediate, and deep), and zone (levels:
from three independent reactions per sample were pooled and north, center, and south). Prior to ANOVA, homogeneity of
sequenced on an Illumina MiSeq using a 2 bp × 250 bp variance was confirmed with Levene’s test (Levene, 1960). All
run (at Fundació per al Foment de la Investigació Sanitària i p-values below 0.05 were considered significant.
Biomédica, FISABIO, Valencia, Spain). Sequences were quality To identify the main environmental factors that explain
filtered removing sequences shorter than 50 bp or with a the changes in the microbial communities among the sampled
Phred quality below 30 by employing prinseq-lite (Schmieder stations, Bray–Curtis distances were calculated using the
and Edwards, 2011), and R1 and R2 reads were joined by “vegdist” function of the “vegan” package, and a NMDS
FLASH (Magoč and Salzberg, 2011) using default parameters. analysis was carried out. SIMPER analysis (Clarke, 1993) was
Assembled sequences were analyzed using Qiime (Caporaso used to identify species potentially responsible for statistically
et al., 2010) for: (i) removing chimeras, using usearch6.1; (ii) significant differences among levels of each factor using “vegan”
clustering sequences in operational taxonomy units (OTUs) (Oksanen, 2011).
with 97% identity, using pick_open_reference_otus.py function; Differences in the multivariate structure of microbial
and (iii) assigning taxonomy of the longest sequence in each communities of each station among sampling times were
OTU, by BLAST against SILVA_132_release database at 97% tested using permutational multivariate analysis of variance
identity. All samples were normalized at 47,461 sequences (the (PERMANOVA) (Anderson, 2001; McArdle and Anderson,
lowest number of sequences in a sample after post-assembly 2001) considering two factors (time and station). Wherein each
and filtering). To visualize the diversity and phylum or class term in the analysis was tested using 4,999 random permutations
abundances at each station and time of sampling, bubble plots of the appropriate units and similarities among samples were
were drawn in R with ggplot2 (Wickham, 2016). calculated using the Bray–Curtis similarity index. Prior to
PERMANOVA, homogeneity of multivariate dispersions among
groups was tested with “betadisper.” All p-values below 0.05
Statistical analysis were considered significant.
To get an explanation concerning the different behavior of
Due to the limitation of analyzing microbiologically the total the microbial communities between the two sampling times
amount of samples collected, and with the aim of selecting in the contaminated and non-contaminated stations, observed
a set of stations representative of all the physicochemical with the above PERMANOVA test, several statistical analyses
and environmental conditions in the Mar Menor sediments, were performed. First, contaminated and non-contaminated
a principal component analysis (PCA) of the environmental stations were defined by clustering the stations by FeA, PbAVS,
variables was carried out using “prcomp.” The environmental and ZnAVS concentrations (indicators of metal pollution)
data were normalized using the function “decostand” of the using the function “agnes” and the ward method of the

“cluster” R package (Supplementary Figure 2) (Maechler AVS concentrations in the Mar Menor bed had been previously
et al., 2019). Then, PERMANOVA with two factors: Time reported (Marín-Guirao et al., 2005) and might be related to a
(levels: March–September) and PTEs [levels: contaminated high sulfate-reducing rate in the sediment favored by the high
(stations 4, 10–14) and non-contaminated (stations 1–3, 5 and content of organic matter and the fine texture (Thode-Andersen
6)] was employed to test for differences in physicochemical and Jørgensen, 1989; Llobet-Brossa et al., 2002). Similarly,
parameters, following the same procedure explained above. high concentrations of PTEs evaluated by means of FeAVS,
Finally, to identify the variables responsible for the differences ZnAVS, PbAVS, CdAVS, and AsAVS were found in almost
reported by PERMANOVA, a two-way ANOVA with the same all the muddy stations in both samplings, with high spatial
factors was tested on each environmental variable. Additionally, variability (Supplementary Table 1.1). Particularly, stations
using SIMPER analysis, metallophilic, intermediate, and non- located in the south of the lagoon (stations 10–14, see Figure 1),
metallophilic OTUs were defined based on the fold change showed significant and unusually high concentrations of PbAVS
among the mean abundance in the contaminated and non- (≈1,000–8,600 mg kg−1 ) and ZnAVS (≈600–3,900 mg kg−1 ).
contaminated stations. Metallophilic OTUs were defined as These results indicated metal(loid) pollution, mainly in the
those having a fold change equal to or higher than 2, southern part of the lagoon, due to the runoff of mine wastes
intermediate OTUs as those with fold change values higher than from the old mining area of Sierra de Cartagena-La Unión, in
0.5 but lower than 2, and non-metallophilic OTUs included agreement with previously reported data (Marín-Guirao et al.,
those with a fold change lower than 0.5. 2008; María-Cervantes et al., 2009). Since PbAVS was correlated
with CdAVS and FeA with FeAVS and ZnAVS, hereinafter we
will only analyze PbAVS and FeA although their individual
Results and discussion effects cannot be distinguished.
General characteristics of the

sediments Microbial abundances
Based on a 3D PCA constructed with the physicochemical Cell concentrations ranged from 6.6 × 107 to 130 × 107
variables, 14 stations (among the 22 sampled stations; cells/g of sediment (Figure 2), values in the ranges previously
Supplementary Figure 1) that covered the variability of reported for other marine sediments (Luna et al., 2002; Sørensen
physicochemical conditions included in the plot, were selected et al., 2007; García-Martínez et al., 2009). Statistically significant
as representative and analyzed more deeply. In these stations, differences in cell concentrations were detected for texture
redox potential (Eh) ranged from 197 to −240 mV with (p = 0.000121), with higher concentrations in muddy than
significantly lower values in muddy than sandy sediments in sandy sediments (42 × 107 to 130 × 107 cells/g vs.
(Supplementary Table 1.1 and Supplementary Figure 3). The 6.6 × 107 to 32 × 107 cells/g) and for zone (p = 0.0131),
Eh was significantly more negative in September than in March but not for time (p = 0.115), depth (p = 0.244), or vegetation
and sulfide (S2− ) presented significantly higher concentrations (p = 0.457) (Supplementary Figure 4). Note that since the
in September, probably reflecting a higher activity of sulfate- sandy samples were only present in the center of the lagoon,
reducing bacteria in the summer as observed in other systems this zone presented lower cell concentrations than the north
(Robador et al., 2009). The pH values varied from nearly and the south. Despite no statistical differences being found
neutral to alkaline (pH: 7.1–8.4), with a tendency to lower for the factor time, it is noteworthy that microbial abundances
values at muddy stations closer to the coast. Soluble organic were higher in September than in March for most of the
carbon (SOC) was significantly higher in vegetated than in studied stations (Figure 2), which is in agreement with
bare sediments with the highest values found in sediments previous studies (Musat et al., 2006; Suárez-Suárez et al.,
colonized by Cymodocea. On the other hand, TOC displayed 2011).
significantly higher concentrations in muddy than in sandy
sediments, mainly in the north. Regarding DOP, which is related
to sulfate reduction (Raiswell et al., 1988), statistically significant Overall microbial community
differences were observed in depth, with the higher values found description
in the deepest sediments, while NH4 + , presented statistically
significant differences between zones, with the higher values The prokaryotic community of the Mar Menor sediments
found in the south. was analyzed by 16S rRNA gene metabarcoding. Although this
Acid volatile sulfide (AVS) was detected in very high is a powerful tool to investigate microbial community structure
concentrations in muddy sediments (≈2.8–141 mg kg−1 ), and dynamics, it has several limitations. For instance, biases due
especially in the south of the lagoon, displaying statistically to different numbers of ribosomal RNA operons (Kembel et al.,
significant differences for both factors (texture and zone). High 2012), choice of amplification primers (Klindworth et al., 2013),

FIGURE 2
Microbial cell concentrations for each Mar Menor sediment station and time of sampling in logarithmic scale. One replicate per station and
sampling time is shown. Error bars indicate standard deviation in DAPI count.
and the amplification process (Suzuki et al., 1998; Sipos et al., The UpSet analysis, considering only OTUs with
2007) have been reported. Furthermore, the bioinformatic relative abundances above 0.1% [the “abundant” biosphere
pipeline is another source of bias, and Qiime1 is known to be (Pedrós-Alió, 2012)], revealed that most of them were specific
very sensitive but usually overestimates diversity (Straub et al., to individual stations with only a small proportion of shared
2020). Additionally, there is the possibility that some of these OTUs (Figure 3B), highlighting the heterogeneity among
OTUs are derived from extracellular DNA from lysed cells (Torti stations. Nevertheless, a core microbiome of nine OTUs was
et al., 2018). We are aware of these limitations and have tried to detected in all stations and sampling times which represented
avoid overreaching conclusions. a substantial fraction of the whole microbial community (from
For the microbiological analyses, DNA was extracted, 2.4 up to 13.8% of total sequences) (Supplementary Table 1.4).
amplified, and sequenced from 82 samples (including triplicates, The previous studies in intertidal sand and marine sediments
except P8 with duplicates). A total of 3,891,802 reads were (Sun et al., 2013; Boehm et al., 2014; Quero et al., 2015) have
obtained and were grouped at 97% of similarity in 324,325 also detected both cosmopolitan (i.e., members of the core) and
OTUs for the 82 samples after quality filtering, clustering, and sample-specific microorganisms, likely representing generalists
normalizing (Supplementary Tables 1.2, 1.3). The rarefaction (i.e., members of the core) and specialists, respectively.
analysis indicated a good recovery of the microbial diversity
inhabiting the sediments although the asymptote was not
reached (Supplementary Figure 5). Regarding alpha diversity, Microbial community structure
the number of OTUs (richness) varied between 7,240 and
15,942, while the Shannon index values ranged from 6.7 to 8.5 Proteobacteria was the phylum most frequently detected
(Figure 3A). The ANOVA test showed statistically significant in all stations, accounting for 20.5–55.8% of the retrieved
differences in richness, and the Shannon index between textures sequences (Supplementary Figure 7), followed by Bacteroidetes
(Shannon p = 0.009773; richness p = 0.001014) and zone and Chloroflexi (4.3–26.4 and 1.9–17%, respectively). At the
(Shannon p = 2.695 × 10−6 ; richness p = 5.91 × 10−6 ), with class level, Deltaproteobacteria (12.7–32.6%), now referred to
higher values in muddy sediments and in the north area of as phylum Desulfobacterota, and Gammaproteobacteria (4.6–
the Mar Menor. However, similar values were found among 30.1%) dominated almost all the stations and times, with the
times (Shannon p = 0.519; richness p = 0.122), depths (Shannon exception of Bacteroidia dominating sample S7 and stations
p = 0.567; richness p = 0.8468), or vegetations (Shannon 1 and 2, both located on the channel connecting the lagoon
p = 0.3696; richness p = 0.329) (Supplementary Figure 6). with the Mediterranean Sea (Figure 4). The previous results
on marine sediments from different locations also indicated

FIGURE 3
(A) Number of OTUs (columns) and Shannon index estimates (dots) for rarefied samples. Deviation bars indicate variability within replicates of
each station and sampling time. (B) Upset plot showing the OTU distribution (for OTUs > 0.1% relative abundance) along the 14 stations during
the cold and warm seasons (March and September, respectively). At the top, columns indicate the number of OTUs shared by stations, which
are marked at the bottom with black dots. Arrow indicates the core microbiome.
the dominance of Proteobacteria and Bacteroidetes (Mahmoudi marine environments (Brinkhoff et al., 2012). This order has
et al., 2015; Quero et al., 2015). been associated with organic matter degradation in the seagrass
Although 16S rRNA gene metabarcoding provides little rhizosphere (Ugarelli et al., 2017) and in Posidonia oceanica
information regarding the metabolic capabilities of the decaying material (Rubio-Portillo et al., 2021). In soil samples,
community (Sun et al., 2020), some putative metabolisms can be members of Myxococcales present an aerobic metabolism,
hypothesized for some of the detected phyla in the Mar Menor although some representatives are anaerobes that respire nitrate
sediments. For instance, the most frequently retrieved orders or Fe (III) (Treude et al., 2003) and produce a wide range of
from the Deltaproteobacteria class were Desulfobacterales and secondary metabolites (Reichenbach, 2015).
Desulfuromonadales, which are typically composed of sulfate- Within the Gammaproteobacteria class, the
and sulfur-reducing bacteria (Madigan et al., 2019). The order Steroidobacterales order was predominant in many stations,
Myxococcales was also abundant in some samples, although mainly due to the abundance of Woeseia, a genus with a
very little is known about their physiology and metabolism in versatile metabolism that goes from sulfur and hydrogen

FIGURE 4
Distribution of bacterial and archaeal classes in Mar Menor sediments. Dot color and size indicate the relative abundance of each class. The
main features of each station are shown at the bottom.
oxidation to chemorganoheterotrophy (Mußmann et al., 2017). In summary, based on the 16S rRNA gene diversity data,
The Chromatiales and Ectothiorhodospirales orders were also assuming all the limitations of this approach (Crosby and
abundant. These groups grow autotrophically, acting as primary Criddle, 2003; Soergel et al., 2012; Ghyselinck et al., 2013; Rubio-
producers, using light and the energy provided by the oxidation Portillo et al., 2016) and the high proportion of OTUs related
of reduced sulfur compounds (Mori et al., 2015; Madigan et al., to uncultured microbes in the analyzed samples, the most
2019; Sorokin et al., 2020). frequently retrieved sequences corresponded to microorganisms
The most frequently retrieved orders of the Bacteroidia class related to S and C cycles, as expected for marine sediments
were Flavobacteriales and Bacteroidales, well-known degraders (Plugge et al., 2011; Urich et al., 2014; Fike et al., 2015).
of polymeric organic matter (Fernández-Gómez et al., 2013; However, Mar Menor sediments also harbored a
Bernardet, 2015; Krieg, 2015). Within this class, some OTUs considerable degree of novelty since several uncultured
could be assigned to genera within Flavobacteriales, which groups were found in relatively high proportions. Sequences
are aerobic or facultative aerobic bacteria with an obligate corresponding to the Asgardeota phylum accounted for up to
chemorganoheterotrophic metabolism (Cho and Giovannoni, 1.7% of the total sequences in some stations. Three classes of this
2004; Kim et al., 2008; Park et al., 2010; Choi et al., phylum, Lokiarchaeia, Heimdallarchaeia, and Odinarchaeia,
2013; Bernardet, 2015). The OTUs assigned to Bacteroidales could be detected at relative abundances of 1.4, 0.3, and 0.2%,
corresponded to uncultured genera, which hampers any respectively. Asgardarchaeota, have been found in different
metabolic inference, although most of the cultured members of aquatic sediments, and are known by their close phylogenetic
this order are strict or facultative anaerobes (Krieg, 2015). relationship with Eukarya, thereby suggesting the emergence of
Considering only nine OTUs that formed the “abundant” eukaryotes within this phylum (Zaremba-Niedzwiedzka et al.,
core microbiome (Figure 3B and Supplementary Table 1.4), 2017; Bulzu et al., 2019). The relative abundance of sequences
sulfate reduction and sulfur oxidation appeared also as related to Heimdallarchaeia, which seems to be the closest
potentially relevant and widespread metabolisms since three of group to eukaryotes (Bulzu et al., 2019; Williams et al., 2020), is
these OTUs belonged to the Desulfobacterales and one to the the highest reported so far.
Chromatiales. Furthermore, two OTUs related to Bacteroidetes Sequences corresponding to the Woesearchaeia class, within
were included in this core, highlighting the putative importance the phylum Nanoarchaeota and now classified as the order
of polymeric organic matter degradation in the system. Woesearchaeales, were present in high proportions, accounting

for up to 5.7% of the community. This group has been detected in aerobic and oligotrophic environments (Oh et al.,
extensively detected around the world in many different 2012, 2016; Mizuno et al., 2015). In summary, these results
ecosystems through 16S rRNA gene sequence studies, but little is suggested that sandy sediments had higher abundances of
known about their ecology and metabolism. The recent studies putatively aerobic microorganisms whereas muddy sediments
have shown the high diversity of this group and pointed to had higher abundances of putatively anaerobic microbes.
the oxic status as the main factor driving the distribution of Regarding the type of benthic vegetation (i.e., Caulerpa
Woesearchaeal members (Liu et al., 2018). A symbiotic or and/or Cymodocea), our result is in good agreement with
syntrophic lifestyle has been proposed although it has not been previous comparisons between seagrasses and macroalgae
confirmed as a general trait of the group (Liu et al., 2018). (Gribben et al., 2017). Curiously, only SOC was statistically
Finally, sequences from the Actinobacteria class WCHB1-81 significant for this factor (Supplementary Figure 3). Given that
accounted for up to 1.1% of the total. This group has been only Caulerpa was able to spread in the Mar Menor due to human
described by 16S rRNA gene analyses so its metabolism remains activity, the taxonomic differences and their corresponding
completely unknown. metabolic potentials are of great importance to determine the
anthropogenic influence on the lagoon. At the class level,
the proportion of sequences related to Deltaproteobacteria
Environmental factors driving was higher in Caulerpa-associated sediments despite not
microbial composition of sediment being statistically significant, while Bacteroidia sequences had
communities a statistically significant higher abundance in Cymodocea-
associated sediments (Figure 6B). The OTUs contributing to
To identify the main environmental factors related with the differences between Caulerpa and Cymodocea communities
the changes in the microbial communities, a NMDS plot based are shown in Supplementary Table 1.6. Our data agree with
on Bray–Curtis distances of the microbial composition and previous observations of higher abundances of sulfate-reducing
abundance was performed. As shown in Figure 5, the texture microorganisms (Deltaproteobacteria) in Caulerpa sediments
(mud vs. sand), the type of vegetation (Caulerpa vs. Cymodocea), compared to phanerogam-colonized ones (Holmer et al., 2009;
the depth (shallow vs. intermediate/deep), and the zone (north Aires et al., 2013; Gribben et al., 2017). Besides the difference
vs south) clustered the samples while factor time did not. in their relative proportions, different families of sulfate
Texture is a well-known factor influencing the microbial reducers were also present in both sediments (Desulfobulbaceae
community composition (Llobet-Brossa et al., 1998; Sun et al., and Desulfobacteraceae in Cymodocea and Caulerpa-colonized
2013) and variables such as Eh, AVS, TOC, AsAVS, and FeA, sediments, respectively). Desulfobacteraceae are considered
which were statistically significant between levels of this factor complete oxidizers while Desulfobulbaceae are unable to oxidize
(Supplementary Figure 3), could be the responsible of this acetate to CO2 (Xing et al., 2020). On the other hand,
differences. Although the influence of texture was expected, different sulfur-oxidizing bacteria were also found associated
information about the relationship between sediment texture with both types of vegetation, with B2M28, Thioalkalivibrio and
and microbial community structure still remains scarce in Thiohalophilus dominating Cymodocea sediments and Woeseia
the literature (Boey et al., 2022). Thus, to provide some and Arenicellaceae prevailing in Caulerpa sediments. The class
light, a detailed analysis of the taxonomic differences was Bacteroidia, which was relatively more abundant in Cymodocea
performed. At the class level, a significant higher relative colonized sediments, has been found to be abundant in other
abundance of Anaerolineae was observed in muddy sediments seagrass species such as Zostera marina, Z. noltii, Thalassia
while sequences related to Bacteroidia, Alphaproteobacteria, testudinum, and Syringodium filliforme, with some phylotypes
and Acidimicrobiia were significantly more abundant in sandy belonging to their core microbiome (Cúcio et al., 2016; Ugarelli
ones (Figure 6A). The most relevant OTUs highlighting the et al., 2019). Furthermore, a study reported an enrichment in
differences between muddy and sandy sediments were identified Bacteroidales inside a patch of the seagrass Zostera compared
by SIMPER (Supplementary Table 1.5). Since microorganisms to the surrounding sediment (Ettinger et al., 2017). These
within the class Anaerolineae are strict anaerobes (Yamada and observations suggest that some kind of stable association, direct
Sekiguchi, 2015), their relatively higher abundances in muddy or indirect, could exist between Bacteroidia and seagrasses, and
sediments with a low redox potential were not surprising. On is probably related to the higher content of labile organic matter
the other hand, sandy sediments showed a more positive redox inside seagrass patches compared to bare sediments (Honkoop
potential and a lower concentration of total organic carbon. et al., 2008; Ricart et al., 2015).
Accordingly, they harbored higher abundances of putatively On the other hand, differences were also observed
aerobic microorganisms, such as the genera Robiginitalea and between the shallowest sediments (0–2 m) and those deeper
Ulvibacter (from the Bacteroidia class) (Cho and Giovannoni, than 2 m. This finding suggests that physicochemical
2004; Choi et al., 2007; Kim et al., 2008), and members conditions change at 2-m depth, shifting microbial
of Alphaproteobacteria and Acidimicrobiia, which have been communities, although only DOP, which was higher in

FIGURE 5
An NMDS plot of the Bray–Curtis distances among all samples (A), colored by factor texture (B), time (C), vegetation (D), depth (E), and zone (F).
FIGURE 6
Relative abundance of detected microbial classes based on the levels of factor texture (A), vegetation (B), depth (C), and zone (D). Error bars
indicate the range of abundances within each group of samples. Mud (n = 66); Sand (n = 16); Cymodocea nodosa (n = 16); C. prolifera (n = 16);
Shallow (n = 46); Intermediate (n = 24); Deep (n = 12); North (n = 18); Centre (n = 34); and South (n = 30). Asterisk (∗ ) indicates statistically
significant differences tested by ANOVA (p < 0.05).
deep sediments, presented statistically significant differences the differences between shallow and intermediate/deep
(Supplementary Figure 3). Intriguingly, a 2-m depth was samples (Supplementary Table 1.7). Remarkably,
also the limit for the survival of vegetation due to anoxia and Desulfobacteraceae were enriched in intermediate/deep
light scarcity during the 2016 algal bloom (Belando et al., samples while Robiginitalea and Actinomarinales were
2017). Regarding the taxonomic differences (Figure 6C), in shallow samples. These differences are similar to
Deltaproteobacteria and Anaerolineae, both well-known those obtained with texture and based on the putative
anaerobic bacteria were significantly more abundant in metabolic potential of these groups are probably due to
intermediate/deep sediments while Bacteroidia, Acidimicrobiia, oxygen availability.
and Alphaproteobacteria were in shallow samples. The Finally, we explored whether the difference between the
SIMPER analysis revealed the OTUs responsible for north and the south microbial communities could be related

to the extremely high concentrations of PTEs found in the of the environmental variables with two factors (time: March
southern basin (Supplementary Figure 3). vs. September; PTEs: contaminated vs. non-contaminated),
indicated that there were significant differences in the whole
lagoon between March and September and between the
Relationships between potentially toxic contaminated and non-contaminated stations but not in the
elements concentrations and microbial interaction between the two factors (Supplementary Table 1.8)
which means that there was no evidence that temporal changes
communities
among the two groups of stations were different and thus,
“hypothesis i” was rejected. Then, the two-way (time and
As explained above, clear differences in the microbial
PTEs) ANOVAs (Supplementary Table 1.9) identified redox
communities were observed between zones, mainly among the
potential and S2− as the variables responsible for temporal
north and south microbial communities (Figure 5E), most
changes, and AVS and PTEs, for the differences between
likely due to the extremely high concentrations of PTEs present
contaminated and non-contaminated stations. Thus, there was
in the southern basin attributable to the presence of mining
no evidence of input of PTEs between March and September
wastes carried from the old mining area (Marín-Guirao et al.,
and therefore “hypothesis ii” was also rejected. The only
2008; María-Cervantes et al., 2009) (Supplementary Figure 3).
environmental variables that differed between contaminated
Remarkably, when the temporal changes in the microbial
and non-contaminated stations were those associated with
communities of each station were tested by PERMANOVA (two
PTEs. Therefore, based on our results, the most likely
factors: station and time) significant p-values were obtained
“hypothesis iii” is that the microbial communities that
(p = 0.0002), and a posteriori test indicated that the stations
inhabit the sediments with high PTEs concentrations are
with the highest PTEs concentrations presented significant
more vulnerable to environmental changes. Further, in vitro
temporal changes while the less contaminated stations did not
experiments would be necessary to confirm the hypothesis.
(Table 1). These differences were mainly due to changes in
Microbes able to survive in the presence of high
low abundance bacterial classes but some relatively abundant
concentrations of PTEs (heavy metals and As), which can
ones (up to 6.2% relative abundance) also displayed extensive
be considered an extreme condition, are known as metallophiles
changes. These differences between the most contaminated (P4,
(Nies, 2000; Gupta et al., 2014). SIMPER analyses supported
P10, P11, P12, P13, and P14) and the less contaminated stations
our hypothesis by revealing that temporal changes in PTE-
(which we will refer to as contaminated and non-contaminated,
contaminated samples were mainly due to metallophilic OTUs
respectively) can be explained by the following three hypotheses:
(defined as those OTUs statistically different or contributing
(i) Contaminated and non-contaminated stations were exposed
to changes among contaminated and non-contaminated
to different temporal environmental changes, (ii) there was an
stations and whose mean relative abundance in contaminated
input of PTEs in the contaminated stations between March
stations was two-fold higher than in non-contaminated
and September, and (iii) microbial communities inhabiting
stations) (19.64–95.15%) (Table 2). Metallophilic OTUs could
the sediments with high PTEs concentrations are more
correspond to specialist bacteria harboring mechanisms to
vulnerable to environmental changes. The PERMANOVA test
resist or use the PTEs which could be more susceptible to
environmental perturbations. Indeed, it has been previously
TABLE 1 The p-values of the PERMANOVA a posteriori test for the
reported that such specialist microorganisms can be more
microbial communities of each station between March and
September. vulnerable to fluctuations in the other environmental variables
since the genetic adaptation to one environment may result
PTEs p (MC)
in loss of fitness in another environment (Cooper and
M1-S1 Non-contaminated 0.1678 Lenski, 2000; Kassen, 2002; Zhong et al., 2004). Nevertheless,
M2-S2 Non-contaminated 0.0724
non-metallophilic OTUs also contributed to temporal changes
M3-S3 Non-contaminated 0.0976
M4-S4 Contaminated 0.0350*
but in a lower proportion (5.44–22.07%).
M5-S5 Non-contaminated 0.1974 Some of the extreme metallophilic OTUs found in the
M6-S6 Non-contaminated 0.1154 Mar Menor sediments have been previously associated with
M7-S7 Non-contaminated 0.0112* metal-rich environments. Metallophiles were identified by
M8-S8 Non-contaminated 0.1802 examining the Upset diagrams, which showed that P10, the
M9-S9 Non-contaminated 0.0472*
most contaminated station, harbored a set of 15 specific
OTUs that were present between March and September with
M12-S12 Contaminated 0.0084* abundances higher than 0.1% (Figure 3B). These OTUs
M13-S13 Contaminated 0.0454* were assigned to Sva1033, Woeseiaceae, Anaerolineaceae,
M14-S14 Contaminated 0.0268* OPB41, Desulfobulbaceae, Desulfuromusa, Flavobacteriaceae,
MC, Monte Carlo correction. *p < 0.05. and SAR324 families. Sva1033 metabolism has been associated

TABLE 2 Percentage of OTUs classified as metallophilic (fold change > 2), intermediate (0.5 < fold change < 2), and non-metallophilic (fold
change < 0.5) that were also statistically different in the PTE contaminated samples between March and September.
Significant OTUs PTE samples vs. time (%)
Significant OTUs among PTE and non-PTE samples Metallophilic (224) 19.64
Intermediate (328) 17.68
Non-metallophilic (1,765) 5.44
OTUs contributing to changes in PTE

samples vs. time (%)
OTUs contributing to changes among PTE and non-PTE samples Metallophilic (1,588) 95.15
Intermediate (3,182) 74.89
Non-metallophilic (2,097) 22.07
Numbers in parenthesis indicate the total number of OTUs within each group.
with metal reduction (Sun et al., 2013; Buongiorno et al., 2019). NCBI database more than 20 years ago and it has been found
Woeseia was the most abundant genus in a copper biofilm even in different ecosystems, there is no available information
(Zhang et al., 2019) and metagenomic data suggested a broad about the metabolism of this class. The high abundance and
range of metabolism for Woeseiaceae, including sulfur-based widespread presence of PAUC43f in the Mar Menor sediments
chemolithoautotrophy (Mußmann et al., 2017). OPB41 refers make it an excellent scenario to study the characteristics of this
to a 16S rRNA gene amplicon sequence detected for the first uncultured class.
time in a Yellowstone hot spring, an environment with high
concentrations of reduced iron and sulfur (Hugenholtz et al.,
1998). Desulfobulbaceae and SAR324 have been reported to Conclusion
negatively correlate with toxic elements (Baltar et al., 2018;
Wu et al., 2019); however, the OTUs detected herein could The Mar Menor lagoon is subjected to natural and intense
be new representatives of these groups since their identities to anthropic pressures, which have left their imprints on the
sequences in the ARB-SILVA database were rather low (95.71 microbial community inhabiting the sediments. Here, we have
and 95.92%, respectively). Flavobacteriaceae was present in toxic shown that texture, type of vegetation, depth, and zone are
metal-contaminated marine sediment (Gillan et al., 2005; Toes strong structuring factors while the effect of time (season)
et al., 2008) and species of the genus Desulfuromusa are well- is more limited and restricted to PTE contaminated stations.
known Fe-reducing bacteria (Vandieken et al., 2006). Our results provide a detailed description of the differences in
Remarkably, two out of the nine core OTUs (those microbial composition associated with these factors which are
shared between all stations and sampling times) with of great importance for the health of the lagoon. For instance,
abundances >0.1% (NR_OTU1827 and AF286033.1.1521) Caulerpa colonized sediments harbor a higher potential for
were also defined as extreme metallophiles and belonged sulfate reduction and thus a lower redox potential (as we
to the classes Gammaproteobacteria and PAUC43f have observed in aquaria experiments, data not shown). This
(Gemmatimonadota phylum), respectively. As shown in human-introduced factor in the Mar Menor can be crucial in
Figure 6D, there were statistically significant higher abundances determining the response of the sediment microbiota to changes
of Gammaprotebacteria and PAUC43f in the south of the in the water column, which may favor the proliferation of
lagoon, the most contaminated area. Sequences similar to this sulfide-producing microbes that negatively affect the system.
Gammaproteobacteria OTU have been detected in heavy metal- However, the sediment microbial community also harbors
rich environments (Ben Said et al., 2010; Meyer-Dombard the potential for detoxification as well as microbes that are
et al., 2012), a microbial mat at a shallow submarine hot spring interesting both because of their novelty and resistance to PTEs.
(Hirayama et al., 2007), and marine sediments (Schöttner et al., The history of mining impacts has most likely influenced the
2011), as well as in the guts of fishes (NCBI accession number microbial communities, which have developed ways to tolerate,
KJ197761). Regarding the PAUC43f 16S rRNA gene sequence and even thrive, in this highly polluted surrounding. However,
(NCBI accession number AF286033), it was first detected in this specialization may have also increased the vulnerability of
a saltmarsh contaminated with mercury and polychlorinated- these communities to other environmental changes which add
biphenyls (PCBs). Closely related sequences were also detected more instability to the whole ecosystem.
in different types of sediments (Bowman and McCuaig, 2003; The sediment microbiota could be a key player in the fate
López-García et al., 2003; Genderjahn et al., 2018) and as a of the Mar Menor since they could buffer the system from, and
symbiont of marine invertebrates (Radwan et al., 2010; Griffiths respond to, environmental changes. Here, we paved the way to
et al., 2019; Bergo et al., 2021). Although it was deposited in the understanding how this may occur.

Data availability statement was also supported by the ACIF fellow of the Generalitat
Valenciana government.
16S rRNA gene sequences generated in this work have been
deposited in the NCBI Sequence Read Archive (SRA) database
under BioProject PRJNA753791.
Acknowledgments
We thank Cristina López–Pascual for her help in the
Author contributions initial processing of the samples and Heather Maughan for
her professional English editing and the critical reading of
BA-R: conceptualization, data curation, formal analysis, the manuscript. We thank Carles Pedrós–Alió for his critical
investigation, methodology, validation, visualization, writing— reading of the manuscript and helpful suggestions. Sediment
original draft, and writing—review and editing. ER-P: sampling and geochemical characterization was carried
data curation, formal analysis, investigation, methodology, out by Universidad Politécnica de Cartagena, Universidad
supervision, validation, visualization, writing—original draft, de Santiago de Compostela, and Centro Oceanográfico de
and writing—review and editing. JÁ-R: conceptualization Murcia (IEO) throughout a contract with TRAGSA, supported
and writing—review and editing. FG-C: conceptualization, by Comunidad Autónoma de Murcia and FEDER funds.
methodology, visualization, and writing—review and Thanks to M. C. Tercero, H. M. Conesa, A. Peñalver, I.
editing. XO: conceptualization, data curation, formal Tunç, B. Straetemans, J. Santos, J. Patricio, J. Roberto, V.
analysis, investigation, methodology, supervision, validation, León, F. Torres, M. Santiso, and P. Guevara for helping
visualization, writing—original draft, and writing—review in sample processing. We acknowledge logistical support
and editing. M-DB: data curation and writing—review and provided by the President and Staff of the harbors Club
editing. JB-E: conceptualization, data curation, funding Nautico Lo Pagán, Club Náutico La Puntica, Centro de
acquisition, methodology, project administration, resources, Actividades Náuticas (San Pedro del Pinatar, Murcia,
and writing—review and editing. RG-M: data curation, Spain), and Club Náutico Los Urrutias. We also thank the
project administration, and writing—review and editing. AF: Regional Government of Murcia and national authorities
data curation, formal analysis, methodology, supervision, (MITECO) for permission.
writing—original draft, and writing—review and editing. JR:
conceptualization, funding acquisition, methodology, project
administration, resources, and writing—review and editing.
FS: conceptualization, investigation, supervision, validation, Conflict of interest
visualization, writing—original draft, and writing—review
and editing. JA: conceptualization, funding acquisition, The authors declare that the research was conducted in the
investigation, project administration, supervision, validation, absence of any commercial or financial relationships that could
visualization, writing—original draft, and writing—review and be construed as a potential conflict of interest.
editing. All authors contributed to the article and approved the
submitted version.
Publisher’s note
Funding All claims expressed in this article are solely those of the
authors and do not necessarily represent those of their affiliated
The study of the microbial communities has been organizations, or those of the publisher, the editors and the
carried out within the project “Metafluidics” and it was reviewers. Any product that may be evaluated in this article, or
funded by the European Union’s framework program claim that may be made by its manufacturer, is not guaranteed
Horizon 2020 (LEIT-BIO-2015-685474 to JA). Samplings or endorsed by the publisher.
were supported by the projects MEMM (financed by
the Spanish Institute of Oceanography), 19-ESMARES2-
ANG (financed by the Spanish Ministry of Ecological
Transition and Demographic Challenge), and BIOFOM Supplementary material
(Ref. TEC0004869 financed by the Regional Government
of Murcia). M-DB and JB-E were supported by a contract The Supplementary Material for this article can be found
within the Program Personal Técnico de Apoyo funded online at: https://www.frontiersin.org/articles/10.3389/fmicb.
by the Ministerio de Economía y Competitividad. BA-R 2022.937683/full#supplementary-material

References
Aguilar-Escribano, J., Mas-Hernández, J., and Ramos-Esplá, A. (2016). Brinkhoff, T., Fischer, D., Vollmers, J., Voget, S., Beardsley, C., Thole, S., et al.
Evaluación del estado y composición de la comunidad fitoplanctónica de las agua (2012). Biogeography and phylogenetic diversity of a cluster of exclusively marine
del mar menor, Murcia (mayo de 2016). Alicante: University of Alicante. myxobacteria. ISME J. 6, 1260–1272. doi: 10.1038/ismej.2011.190
Aires, T., Serrão, E. A., Kendrick, G., Duarte, C. M., and Arnaud-Haond, S. Bulzu, P. A., Andrei, A. Ş., Salcher, M. M., Mehrshad, M., Inoue, K., Kandori, H.,
(2013). Invasion is a community affair: Clandestine followers in the bacterial et al. (2019). Casting light on Asgardarchaeota metabolism in a sunlit microoxic
community associated to green algae, Caulerpa racemosa, track the invasion niche. Nat. Microbiol. 4, 1129–1137. doi: 10.1038/s41564-019-0404-y
source. PLoS One 8:e68429. doi: 10.1371/journal.pone.0068429
Buongiorno, J., Herbert, L. C., Wehrmann, L. M., Michaud, A. B., Laufer, K.,
Alongi, D. M. (1994). The role of bacteria in nutrient recycling in tropical Røy, H., et al. (2019). Complex microbial communities drive iron and sulfur
mangrove and other coastal benthic ecosystems. Hydrobiologia 285, 19–32. doi: cycling in Arctic fjord sediments. Appl. Environ. Microbiol. 85:e00949-19. doi:
10.1007/BF00005650 10.1128/AEM.00949-19
Alongi, D. M. (1998). Coastal ecosystem processes. Boca Raton, FL: CRC press. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D.,
Costello, E. K., et al. (2010). QIIME allows analysis of high-throughput community
Álvarez-Rogel, J., Santos, J., Belando, M. D., and Bernardeau, J. (2019). Proyecto
sequencing data. Nat. Methods 7, 335–336. doi: 10.1038/nmeth.f.303
BIOFOM. Estudio biogeoquímico de los fondos del mar menor- caracterización
biológica de sedimentos (Ref. TEC0004869). Encomienda de Gestión de la CARM Cho, J. C., and Giovannoni, S. J. (2004). Robiginitalea biformata gen. nov., sp.
a través de Tecnologías y Servicios Agrarios, S.A., S.M.E., M.P. (TRAGSATEC). nov., a novel marine bacterium in the family Flavobacteriaceae with a higher G +
C content. Int. J. Syst. Evol. Microbiol. 54, 1101–1106. doi: 10.1099/ijs.0.03023-0
Anderson, M. J. (2001). A new method for non-parametric multivariate analysis
of variance. Austral Ecol. 26, 32–46. doi: 10.1046/j.1442-9993.2001.01070.x Choi, A., Yang, S. J., and Cho, J. C. (2013). Lutibacter flavus sp. nov., a marine
bacterium isolated from a tidal flat sediment. Int. J. Syst. Evol. Microbiol. 63,
AOAC (1975). Official methods of analysis, 12th Edn. Arlington, VA: AOAC
946–951. doi: 10.1099/ijs.0.043471-0
International.
Choi, T. H., Lee, H. K., Lee, K., and Cho, J. C. (2007). Ulvibacter antarcticus
Aravio-Torre, J., and Arévalo, A. (1973). La salinidad del Mar Menor, sus
sp. nov., isolated from Antarctic coastal seawater. Int. J. Syst. Evol. Microbiol. 64,
variaciones. Algunas consideraciones sobre el intercambio de aguas con el
2041–2046. doi: 10.1099/ijs.0.65265-0
Mediterráneo. Boll. Inst. Esp. Ocean 146, 1–13.
Clarke, K. R. (1993). Non-parametric multivariate analyses of changes in
Ballester, R. (1985). Biomasa, estacionalidad y distribución de tres macrófitos:
community structure. Aust. J. Ecol. 18, 117–143.
Ruppia cirrhosa, Cymodocea nodosa y Caulerpa prolifera en el Mar Menor (Murcia,
SE de España). An. Biol. 4, 31–36. Cline, J. D. (1969). Spectrophotometric determination of hydrogen sulfide in
natural waters. Limnol. Oceanogr. 14, 454–458. doi: 10.4319/lo.1969.14.3.0454
Baltar, F., Gutiérrez-Rodríguez, A., Meyer, M., Skudelny, I., Sander, S.,
Thomson, B., et al. (2018). Specific effect of trace metals on marine heterotrophic Conesa, H. M., and Jiménez-Cárceles, F. J. (2007). The Mar Menor lagoon (SE
microbial activity and diversity: Key role of iron and zinc and hydrocarbon- Spain): A singular natural ecosystem threatened by human activities. Mar. Pollut.
degrading bacteria. Front. Microbiol. 9:3190. doi: 10.3389/fmicb.2018. Bull. 54, 839–849. doi: 10.1016/j.marpolbul.2007.05.007
03190
Conesa, H. M., and Schulin, R. (2010). The Cartagena-La Unión mining district
Barbier, E., Hacker, S., Kennedy, C., Koch, E., Stier, A., and Silliman, B. (2011). (SE spain): A review of environmental problems and emerging phytoremediation
The value of estuarine and coastal ecosystem services. Ecol. Monogr. 81, 169–193. solutions after fifteen years research. J. Environ. Monit. 12, 1225–1233. doi: 10.
1039/c000346h
Belando, M. D., Bernardeau-Esteller, J., García-Muñoz, R., Ramos-Segura, A.,
Santos-Echeandía, J., García-Moreno, P., et al. (2017). Evaluación del estado de Conway, J. R., Lex, A., and Gehlenborg, N. (2017). UpSetR: An R package
conservación de las praderas de Cymodocea nodosa en la laguna costera del Mar for the visualization of intersecting sets and their properties. Bioinformatics 33,
Menor. 2014-2016. Murcia: Instituto Español de Oceanografía y Asociación de 2938–2940. doi: 10.1093/bioinformatics/btx364
Naturalistas del Sureste.
Cooper, V. S., and Lenski, R. E. (2000). The population genetics of ecological
Belando, M. D., Bernardeau-Esteller, J., Paradinas, I., Ramos-Segura, A., specialization in evolving Escherichia coli populations. Nature 407, 736–739. doi:
García-Muñoz, R., García-Moreno, et al. (2021). Long-term coexistence between 10.1038/35037572
the macroalga Caulerpa prolifera and the seagrass Cymodocea nodosa in a
Crosby, L. D., and Criddle, C. S. (2003). Understanding bias in microbial
Mediterranean lagoon. Aquat. Bot. 173:103415. doi: 10.1016/j.aquabot.2021.
community analysis techniques due to rrn operon copy number heterogeneity.
103415
Biotechniques 34, 790–802. doi: 10.2144/03344rr01
Belando-Torrente, M. D., Ruiz, J. M., Muñoz, R., Segura, A., Esteller, J., Casero,
Cúcio, C., Engelen, A. H., Costa, R., and Muyzer, G. (2016). Rhizosphere
J., et al. (2019). Collapse of macrophytic communities in a eutrophicated coastal
microbiomes of European seagrasses are selected by the plant, but are not species
lagoon. Front. Mar. Sci. 6:192. doi: 10.3389/conf.fmars.2019.08.00192
specific. Front. Microbiol. 7:440. doi: 10.3389/fmicb.2016.00440
Ben Said, O., Goñi-Urriza, M., El Bour, M., Aissa, P., and Duran, R. (2010).
De Wit, R., Stal, L. J., Lomstein, B. A., Herbert, R. A., Van Gemerden, H., Viaroli,
Bacterial community structure of sediments of the bizerte lagoon (Tunisia), a
P., et al. (2001). Robust: The role of buffering capacities in stabilising coastal lagoon
southern mediterranean coastal anthropized lagoon. Microb. Ecol. 59, 445–456.
ecosystems. Cont. Shelf Res. 21, 2021–2041. doi: 10.1016/S0278-4343(01)00040-1
doi: 10.1007/s00248-009-9585-x
DeLong, E. F., Taylor, L. T., Marsh, T. L., and Preston, C. M. (1999).
Bergo, N. M., Bendia, A. G., Ferreira, J. C. N., Murton, B. J., Brandini, F. P., and
Visualization and enumeration of marine planktonic archaea and bacteria by using
Pellizari, V. H. (2021). Microbial diversity of deep-sea ferromanganese crust field
polyribonucleotide probes and fluorescent in situ hybridization. Appl. Environ.
in the Rio Grande rise, southwestern Atlantic ocean. Microb. Ecol. 82, 344–355.
Microbiol. 65, 5554–5563. doi: 10.1128/aem.65.12.5554-5563.1999
doi: 10.1007/s00248-020-01670-y
Eilers, H., Pernthaler, J., Glöckner, F. O., and Amann, R. (2000). Culturability
Bernardet, J.-F. (2015). “Flavobacteriales ord. nov,” in Bergey’s manual of
and in situ abundance of pelagic Bacteria from the North Sea. Appl. Environ.
systematics of archaea and bacteria, eds M. E. Trujillo, S. Dedysh, P. DeVos,
Microbiol. 66, 3044–3051. doi: 10.1128/AEM.66.7.3044-3051.2000
B. Hedlund, P. Kämpfer, F. A. Rainey, et al. (New York, NY: Springer), 1–2.
doi: 10.1002/9781118960608.obm00033 Ettinger, C. L., Voerman, S. E., Lang, J. M., Stachowicz, J. J., and Eisen, J. A.
(2017). Microbial communities in sediment from Zostera marina patches, but not
Boehm, A. B., Yamahara, K. M., and Sassoubre, L. M. (2014). Diversity
the Z. marina leaf or root microbiomes, vary in relation to distance from patch
and transport of microorganisms in intertidal sands of the california
edge. PeerJ 5:e3246. doi: 10.7717/peerj.3246
coast. Appl. Environ. Microbiol. 80, 3943–3951. doi: 10.1128/AEM.00
513-14 Fernández-Gómez, B., Richter, M., Schüler, M., Pinhassi, J., Acinas, S. G.,
González, J. M., et al. (2013). Ecology of marine bacteroidetes: A comparative
Boey, J. S., Mortimer, R., Couturier, A., Worrallo, K., and Handley, K. M.
genomics approach. ISME J. 7, 1026–1037. doi: 10.1038/ismej.2012.169
(2022). Estuarine microbial diversity and nitrogen cycling increase along sand–
mud gradients independent of salinity and distance. Environ. Microbiol. 24, 50–65. Fike, D. A., Bradley, A. S., and Rose, C. V. (2015). Rethinking the ancient sulfur
doi: 10.1111/1462-2920.15550 cycle. Annu. Rev. Earth Planet. Sci. 43, 593–622. doi: 10.1146/annurev-earth-
060313-054802
Bowman, J. P., and McCuaig, R. D. (2003). Biodiversity, community structural
shifts, and biogeography of prokaryotes within Antarctic continental shelf Fortin, D., Leppard, G. G., and Tessier, A. (1993). Characteristics of lacustrine
sediment. Appl. Environ. Microbiol. 69, 2463–2483. doi: 10.1128/AEM.69.5.2463- diagenetic iron oxyhydroxides. Geochim. Cosmochim. Acta 57, 4391–4404. doi:
2483.2003 10.1016/0016-7037(93)90490-N

Fraile-Nuez, E., Machín, F., Santana-Casiano, J. M., González-Dávila, M., and abundance. PLoS Comput. Biol. 8:e1002743. doi: 10.1371/journal.pcbi.100
Domínguez-Yanes, J. F., Mercado, J., et al. (2018). Estudio oceanográfico integral 2743
de alta resolución de la laguna costera de El Mar Menor. Murcia: Instituto Español
Kim, J. H., Kim, K. Y., Hahm, Y. T., Kim, B. S., Chun, J., and Cha, C. J.
de Oceanografía y Asociación de Naturalistas del Sureste.
(2008). Actibacter sediminis gen. nov., sp. nov., a marine bacterium of the family
García, G., and Muñoz-Vera, A. (2015). Characterization and evolution of the Flavobacteriaceae isolated from tidal flat sediment. Int. J. Syst. Evol. Microbiol. 58,
sediments of a Mediterranean coastal lagoon located next to a former mining area. 139–143. doi: 10.1099/ijs.0.65346-0
Mar. Pollut. Bull. 100, 249–263. doi: 10.1016/j.marpolbul.2015.08.042
Kjerfve, B. (1994). Chapter 1 coastal lagoons. Elsevier Oceanogr. Ser. 60, 1–8.
García-Martínez, M., López-López, A., Calleja, M. L., Marbà, N., and Duarte, doi: 10.1016/S0422-9894(08)70006-0
C. M. (2009). Bacterial community dynamics in a seagrass (Posidonia oceanica)
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., et al.
meadow sediment. Estuaries Coast. 32, 276–286. doi: 10.1007/s12237-008-9115-y
(2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical
Genderjahn, S., Alawi, M., Mangelsdorf, K., Horn, F., and Wagner, D. (2018). and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41:e1.
Desiccation-and saline-tolerant bacteria and archaea in kalahari pan sediments. doi: 10.1093/nar/gks808
Front. Microbiol. 9:2082. doi: 10.3389/fmicb.2018.02082
Kostka, J. E., and Luther, G. W. (1994). Partitioning and speciation of solid
Ghai, R., Hernandez, C. M., Picazo, A., Mizuno, C. M., Ininbergs, K., Díez, phase iron in saltmarsh sediments. Geochim. Cosmochim. Acta 58, 1701–1710.
B., et al. (2012). Metagenomes of mediterranean coastal lagoons. Sci. Rep. 2:490. doi: 10.1016/0016-7037(94)90531-2
doi: 10.1038/srep00490
Krieg, N. R. (ed.). (2015). “Bacteroidales ord. nov,” in Bergey’s manual of
Ghyselinck, J., Pfeiffer, S., Heylen, K., Sessitsch, A., and De Vos, P. (2013). The systematics of archaea and bacteria, (Hoboken, NJ: John Wiley & Sons, Inc).
effect of primer choice and short read sequences on the outcome of 16S rRNA gene doi: 10.1002/9781118960608.obm00028
based diversity studies. PLoS One 8:e71360. doi: 10.1371/journal.pone.0071360
León, V. M., García, I., González, E., Samper, R., Fernández-González, V.,
Gilabert, J. (2001). Seasonal plankton dynamics in a Mediterranean hypersaline and Muniategui-Lorenzo, S. (2018). Potential transfer of organic pollutants from
coastal lagoon: The Mar Menor. J. Plankton Res. 23, 207–218. doi: 10.1093/plankt/ littoral plastics debris to the marine environment. Environ. Pollut. 236, 442–453.
23.2.207 doi: 10.1016/j.envpol.2018.01.114
Gillan, D. C., Danis, B., Pernet, P., Joly, G., and Dubois, P. (2005). Structure of León, V. M., Moreno-González, R., García, V., and Campillo, J. A. (2017).
sediment-associated microbial communities along a heavy-metal contamination Impact of flash flood events on the distribution of organic pollutants in surface
gradient in the marine environment. Appl. Environ. Microbiol. 71, 679–690. doi: sediments from a Mediterranean coastal lagoon (Mar Menor, SE Spain). Environ.
10.1128/AEM.71.2.679-690.2005 Sci. Pollut. Res. 24, 4284–4300. doi: 10.1007/s11356-015-4628-y
Gomariz, M., Martínez-García, M., Santos, F., Rodríguez, F., Capella-Gutiérrez, León, V. M., Moreno-González, R., González, E., Martínez, F., García, V.,
S., Gabaldón, T., et al. (2015). From community approaches to single-cell and Campillo, J. A. (2013). Interspecific comparison of polycyclic aromatic
genomics: The discovery of ubiquitous hyperhalophilic Bacteroidetes generalists. hydrocarbons and persistent organochlorines bioaccumulation in bivalves from a
ISME J. 9, 16–31. doi: 10.1038/ismej.2014.95 Mediterranean coastal lagoon. Sci. Total Environ. 463–464, 975–987. doi: 10.1016/
j.scitotenv.2013.06.075
Gribben, P. E., Nielsen, S., Seymour, J. R., Bradley, D. J., West, M. N., and
Thomas, T. (2017). Microbial communities in marine sediments modify success Levene, H. (1960). Robust tests for equality of variances. Redwood City, CA:
of an invasive macrophyte. Sci. Rep. 7:9845. doi: 10.1038/s41598-017-10231-2 Stanford University Press.
Griffiths, S. M., Antwis, R. E., Lenzi, L., Lucaci, A., Behringer, D. C., Butler, M. J., Liu, X., Li, M., Castelle, C. J., Probst, A. J., Zhou, Z., Pan, J., et al. (2018). Insights
et al. (2019). Host genetics and geography influence microbiome composition in into the ecology, evolution, and metabolism of the widespread woesearchaeotal
the sponge Ircinia campana. J. Anim. Ecol. 88, 1684–1695. doi: 10.1111/1365-2656. lineages. Microbiome 6:102. doi: 10.1186/s40168-018-0488-2
13065
Llobet-Brossa, E., Rabus, R., Böttcher, M. E., Könneke, M., Finke, N., Schramm,
Gupta, G. N., Srivastava, S., Khare, S. K., and Prakash, V. (2014). Extremophiles: A., et al. (2002). Community structure and activity of sulfate-reducing bacteria in
An overview of microorganism from extreme environment. Int. J. Agric. Environ. an intertidal surface sediment: A multi-method approach. Aquat. Microb. Ecol. 29,
Biotechnol. 7, 371–380. doi: 10.5958/2230-732x.2014.00258.7 211–226. doi: 10.3354/ame029211
Hewson, I., and Fuhrman, J. A. (2008). “Viruses, bacteria, and the microbial Llobet-Brossa, E., Rosselló-Mora, R., and Amann, R. (1998). Microbial
loop,” in Nitrogen in the Marine Environment, eds D. Capone, D. Bronk, M. community composition of wadden sea sediments as revealed by fluorescence
Mulholland, and E. Carpenter (Amsterdam: Elsevier), 1097–1134. doi: 10.1016/ in situ hybridization. Appl. Environ. Microbiol. 64, 2691–2696. doi: 10.1128/aem.
B978-0-12-372522-6.00025-6 64.7.2691-2696.1998
Hirayama, H., Sunamura, M., Takai, K., Nunoura, T., Noguchi, T., Oida, H., López-García, P., Duperron, S., Philippot, P., Foriel, J., Susini, J., and
et al. (2007). Culture-dependent and -independent characterization of microbial Moreira, D. (2003). Bacterial diversity in hydrothermal sediment and
communities associated with a shallow submarine hydrothermal system occurring epsilonproteobacterial dominance in experimental microcolonizers at the Mid-
within a coral reef off Taketomi Island, Japan. Appl. Environ. Microbiol. 73, Atlantic Ridge. Environ. Microbiol. 5, 961–976. doi: 10.1046/j.1462-2920.2003.00
7642–7656. doi: 10.1128/AEM.01258-07 495.x
Holmer, M., Marbà, N., Lamote, M., and Duarte, C. M. (2009). Deterioration of Luna, G. M., Manini, E., and Danovaro, R. (2002). Large fraction of dead
sediment quality in seagrass meadows (Posidonia oceanica) invaded by macroalgae and inactive bacteria in coastal marine sediments: Comparison of protocols for
(Caulerpa sp.). Estuaries Coast. 32, 456–466. doi: 10.1007/s12237-009-9133-4 determination and ecological significance. Appl. Environ. Microbiol. 68, 3509–
3513. doi: 10.1128/AEM.68.7.3509-3513.2002
Honkoop, P. J. C., Berghuis, E. M., Holthuijsen, S., Lavaleye, M. S. S., and
Piersma, T. (2008). Molluscan assemblages of seagrass-covered and bare intertidal Madigan, M., Bender, K., Buckley, D., Sattley, W., and Stahl, D. (2019). Brock
flats on the Banc d’Arguin, Mauritania, in relation to characteristics of sediment biology of microorganisms, 15th Edn. London: Pearson.
and organic matter. J. Sea Res. 60, 255–263. doi: 10.1016/j.seares.2008.10.001
Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M., Hornik, K., Studer, M., et al.
Hugenholtz, P., Pitulle, C., Hershberger, K. L., and Pace, N. R. (1998). Novel (2019). Package “cluster” for R: ‘Finding Groups in Data’: Cluster Analysis Extended.
division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180,
Magoč, T., and Salzberg, S. L. (2011). FLASH: Fast length adjustment of short
366–376. doi: 10.1128/jb.180.2.366-376.1998
reads to improve genome assemblies. Bioinformatics 27, 2957–2963. doi: 10.1093/
Jiménez-Cárceles, F. J., Egea, C., Rodríguez-Caparrós, A. B., Barbosa, O. A., bioinformatics/btr507
Delgado, M. J., Ortiz, R., et al. (2006). Contents of nitrogen, ammonium,
MAGRAMA (2008). Ministerio de agricultura, alimentación y medio ambiente.
phosphorus, pesticides and heavy metals, in a salt marsh in the coast of the Mar
Available online at: https://www.miteco.gob.es/es/costas/temas/proteccion-costa/
Menor lagoon (SE Spain). Fresenius Environ. Bull. 15, 370–378.
ecocartografias/ecocartografia-murcia.aspx
Jiménez-Martinez, J., Garcia-Aróstegui, J. L., Hunink, J. E., Contreras, S.,
Mahmoudi, N., Robeson, M. S. II, Castro, H. F., Fortney, J. L., Techtmann,
Baudron, P., and Candela, L. (2016). The role of groundwater in highly human-
S. M., Joyner, D. C., et al. (2015). Microbial community composition and diversity
modified hydrosystems: A review of impacts and mitigation options in the Campo
in Caspian Sea sediments. FEMS Microbiol. Ecol. 91, 1–11. doi: 10.1093/femsec/
de Cartagena-Mar Menor coastal plain (SE Spain). Environ. Rev. 24, 377–392.
fiu013
Kassen, R. (2002). The experimental evolution of specialists, generalists, and the
María-Cervantes, A., Jiménez-Cárceles, F. J., and Álvarez-Rogel, J. (2009). As,
maintenance of diversity. J. Evol. Biol. 15, 173–190. doi: 10.1046/j.1420-9101.2002.
Cd, Cu, Mn, Pb, and Zn contents in sediments and mollusks (Hexaplex trunculus
00377.x
and Tapes decussatus) from coastal zones of a mediterranean lagoon (mar menor,
Kembel, S. W., Wu, M., Eisen, J. A., and Green, J. L. (2012). Incorporating SE Spain) affected by mining wastes. Water Air Soil Pollut. 200, 289–304. doi:
16S gene copy number information improves estimates of microbial diversity 10.1007/s11270-008-9913-7

Marín-Guirao, L., Atucha, A. M., Barba, J. L., López, E. M., and García Oksanen, J. (2011). Multivariate analysis of ecological communities in R:
Fernández, A. J. (2005). Effects of mining wastes on a seagrass ecosystem: Metal Vegan tutorial. Available Online at: https://cran.r-project.org/web/packages/
accumulation and bioavailability, seagrass dynamics and associated community vegan/index.html (accessed June 27, 2019).
structure. Mar. Environ. Res. 60, 317–337. doi: 10.1016/j.marenvres.2004.11.002
Park, S., Kang, S. J., Oh, T. K., and Yoon, J. H. (2010). Lutibacter maritimus sp.
Marín-Guirao, L., Bernardeau-Esteller, J., Belando, M. D., Cerezo, I., Pérez, E., nov., isolated from a tidal flat sediment. Int. J. Syst. Evol. Microbiol. 60, 610–614.
Ramos, A., et al. (2019). Physiological tipping points to light reduction underlie doi: 10.1099/ijs.0.012401-0
seagrass population collapse and abrupt shift in a shallow coastal lagoon. Front.
Pedrós-Alió, C. (2012). The rare bacterial biosphere. Ann. Rev. Mar. Sci. 4,
Mar. Sci. 6:181. doi: 10.3389/conf.fmars.2019.08.00181
449–466. doi: 10.1146/annurev-marine-120710-100948
Marín-Guirao, L., Lloret, J., and Marin, A. (2008). Carbon and nitrogen stable
Pérez-Ruzafa, A., Campillo, S., Fernández-Palacios, J. M., García-Lacunza, A.,
isotopes and metal concentration in food webs from a mining-impacted coastal
García-Oliva, M., Ibañez, H., et al. (2019). Long-term dynamic in nutrients,
lagoon. Sci. Total Environ. 393, 118–130. doi: 10.1016/j.scitotenv.2007.12.023
chlorophyll a, and water quality parameters in a coastal lagoon during a process of
Mas, J. (1994). El Mar menor: Relaciones, diferencias y afinidades entre la laguna eutrophication for decades, a sudden break and a relatively rapid recovery. Front.
costera y el Mar Mediterráneo adyacente. Ph.D. Thesis. Madrid: Autonomous Mar. Sci. 6:26. doi: 10.3389/fmars.2019.00026
University of Madrid.
Pérez-Ruzafa, A., and Marcos, C. (2012). Fisheries in coastal lagoons: An
McArdle, B. H., and Anderson, M. J. (2001). Fitting multivariate models to assumed but poorly researched aspect of the ecology and functioning of coastal
community data: A comment on distance-based redundancy analysis. Ecology 82, lagoons. Estuar. Coast. Shelf Sci. 110, 15–31. doi: 10.1016/j.ecss.2012.05.025
290–297.
Pérez-Ruzafa, A., Quispe-Becerra, J. I., García-Charton, J. A., and Marcos,
McMurdie, P. J., and Holmes, S. (2013). Phyloseq: An R package for C. (2004). Composition, structure and distribution of the ichthyoplankton in a
reproducible interactive analysis and graphics of microbiome census data. PLoS Mediterranean coastal lagoon. J. Fish Biol. 64, 202–218. doi: 10.1111/j.1095-8649.
One 8:e61217. doi: 10.1371/journal.pone.0061217 2004.00301.x
Mercado, J. M., Cortés, D., Gómez-Jakobsen, F., García-Gómez, C., Petro, C., Zäncker, B., Starnawski, P., Jochum, L. M., Ferdelman, T. G.,
Ouaissa, S., Yebra, L., et al. (2021). Role of small-sized phytoplankton in Jørgensen, B. B., et al. (2019). Marine deep biosphere microbial communities
triggering an ecosystem disruptive algal bloom in a Mediterranean hypersaline assemble in near-surface sediments in Aarhus Bay. Front. Microbiol. 10:758. doi:
coastal lagoon. Mar. Pollut. Bull. 164:111989. doi: 10.1016/j.marpolbul.2021. 10.3389/fmicb.2019.00758
111989
Plugge, C. M., Zhang, W., Scholten, J. C. M., and Stams, A. J. M. (2011).
Meyer-Dombard, D. R., Price, R. E., Pichler, T., and Amend, J. P. (2012). Metabolic flexibility of sulfate-reducing bacteria. Front. Microbiol. 2:81. doi: 10.
Prokaryotic populations in arsenic-rich shallow-sea hydrothermal sediments of 3389/fmicb.2011.00081
Ambitle island, Papua New Guinea. Geomicrobiol. J. 29, 1–17. doi: 10.1080/
Quero, G. M., Cassin, D., Botter, M., Perini, L., and Luna, G. M. (2015). Patterns
01490451.2010.520073
of benthic bacterial diversity in coastal areas contaminated by heavy metals,
Mizuno, C. M., Rodriguez-Valera, F., and Ghai, R. (2015). Genomes of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs).
planktonic acidimicrobiales: Widening horizons for marine actinobacteria by Front. Microbiol. 6:1053. doi: 10.3389/fmicb.2015.01053
metagenomics. mBio 6:02083-14. doi: 10.1128/mBio.02083-14
Radwan, M., Hanora, A., Zan, J., Mohamed, N. M., Abo-Elmatty, D. M., Abou-
Moreno-González, R., Rodríguez-Mozaz, S., Gros, M., Pérez-Cánovas, E., El-Ela, S. H., et al. (2010). Bacterial community analyses of two red sea sponges.
Barceló, D., and León, V. M. (2014). Input of pharmaceuticals through coastal Mar. Biotechnol. 12, 350–360. doi: 10.1007/s10126-009-9239-5
surface watercourses into a Mediterranean lagoon (Mar Menor, SE Spain): Sources
and seasonal variations. Sci. Total Environ. 490, 59–72. doi: 10.1016/j.scitotenv. Raiswell, R., Buckley, F., Berner, R. A., and Anderson, T. F. (1988). Degree
2014.04.097 of pyritization of iron as a paleoenvironmental indicator of bottom-water
oxygenation. J. Sediment. Res. 58, 812–819. doi: 10.1306/212F8E72-2B24-11D7-
Moreno-González, R., Rodríguez-Mozaz, S., Huerta, B., Barceló, D., and León, 8648000102C1865D
V. M. (2016). Do pharmaceuticals bioaccumulate in marine molluscs and fish from
a coastal lagoon? Environ. Res. 146, 282–298. doi: 10.1016/j.envres.2016.01.001 Raiswell, R., Canfield, D. E., and Berner, R. A. (1994). A comparasion of iron
extraction methods of degree of pyritisation and the recognition of iron-limited
Mori, K., Suzuki, K. I., Yamaguchi, K., Urabe, T., and Hanada, S. (2015). formation. Chem. Geol. 111, 101–110. doi: 10.1016/0009-2541(94)90084-1
Thiogranum longum gen. nov., sp. nov., an obligately chemolithoautotrophic,
sulfur-oxidizing bacterium of the family Ectothiorhodospiraceae isolated from Reichenbach, H. (2015). “Myxococcales,” in Bergey’s manual of systematics of
a deep-sea hydrothermal field, and an emended description of the genus archaea and bacteria, eds W. B. Whitman, F. Rainey, P. Kämpfer, M. Trujillo, J.
Thiohalomonas. Int. J. Syst. Evol. Microbiol. 65, 235–241. doi: 10.1099/ijs.0.070 Chun, P. DeVos, B. Hedlund, and S. Dedysh (Hoboken, NJ: John Wiley & Sons,
599-0 Inc), 1–31. doi: 10.1002/9781118960608.obm00088
Muñoz-Vera, A., García, G., and García-Sánchez, A. (2015). Metal Ricart, A. M., York, P. H., Rasheed, M. A., Pérez, M., Romero, J., Bryant,
bioaccumulation pattern by Cotylorhiza tuberculata (Cnidaria, Scyphozoa) C. V., et al. (2015). Variability of sedimentary organic carbon in patchy seagrass
in the Mar Menor coastal lagoon (SE Spain). Environ. Sci. Pollut. Res. 22, landscapes. Mar. Pollut. Bull. 100, 476–482. doi: 10.1016/j.marpolbul.2015.09.032
19157–19169. doi: 10.1007/s11356-015-5119-x
Robador, A., Brüchert, V., and Jørgensen, B. B. (2009). The impact of
Musat, N., Werner, U., Knittel, K., Kolb, S., Dodenhof, T., van Beusekom, J. E. E., temperature change on the activity and community composition of sulfate-
et al. (2006). Microbial community structure of sandy intertidal sediments in the reducing bacteria in arctic versus temperate marine sediments. Environ. Microbiol.
North Sea, Sylt-Rømø Basin, Wadden Sea. Syst. Appl. Microbiol. 29, 333–348. 11, 1692–1703. doi: 10.1111/J.1462-2920.2009.01896.X
doi: 10.1016/j.syapm.2005.12.006
Romero, D., Barcala, E., María-Dolores, E., and Muñoz, P. (2020). European
Mußmann, M., Pjevac, P., Krüger, K., and Dyksma, S. (2017). Genomic eels and heavy metals from the Mar Menor lagoon (SE Spain). Mar. Pollut. Bull.
repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members 158:111368. doi: 10.1016/j.marpolbul.2020.111368
of microbial communities in marine sediments. ISME J. 11, 1276–1281. doi: 10.
Rubio-Portillo, E., Martin-Cuadrado, A.-B., Ramos-Esplá, A. Á., and Antón,
1038/ismej.2016.185
J. (2021). Metagenomics unveils Posidonia oceanica “banquettes” as a potential
Neiker. (2005). Determinación del contenido de amonio en aguas, lixiviados y source of novel bioactive compounds and carbohydrate active enzymes
extractos. (PEC/EN/A-059). (CAZymes). mSystems 6:e00866-21. doi: 10.1128/msystems.00866-21
Newton, A., Brito, A. C., Icely, J. D., Derolez, V., Clara, I., Angus, S., et al. (2018). Rubio-Portillo, E., Santos, F., Martínez-García, M., de los Ríos, A., Ascaso, C.,
Assessing, quantifying and valuing the ecosystem services of coastal lagoons. Souza-Egipsy, V., et al. (2016). Structure and temporal dynamics of the bacterial
J. Nat. Conserv. 44, 50–65. doi: 10.1016/J.JNC.2018.02.009 communities associated to microhabitats of the coral Oculina patagonica. Environ.
Microbiol. 18, 4564–4578. doi: 10.1111/1462-2920.13548
Nies, D. H. (2000). Heavy metal-resistant bacteria as extremophiles: Molecular
physiology and biotechnological use of Ralstonia sp. CH34. Extremophiles 4, Ruiz, J. M., Albentosa, M., Aldeguer, B., Álvarez-Rogel, J., Antón, J., Belando,
77–82. doi: 10.1007/s007920050140 M. D., et al. (2020). Informe de evolución y estado actual del Mar Menor en relación
al proceso de eutrofización y sus causas. Informe de asesoramiento técnico del
Oh, K. H., Choi, W. C., Jung, Y. T., Kang, S. J., Oh, T. K., and Yoon, J. H. (2012).
Instituto Español de Oceanografía.
Tropicimonas aquimaris sp. nov., isolated from seawater, and emended description
of the genus Tropicimonas Harwati et al. 2009. Int. J. Syst. Evol. Microbiol. 62, Schmieder, R., and Edwards, R. (2011). Quality control and preprocessing of
688–692. doi: 10.1099/ijs.0.029371-0 metagenomic datasets. Bioinformatics 27, 863–864. doi: 10.1093/bioinformatics/
btr026
Oh, M., Kim, J. H., and Kim, W. (2016). Tropicimonas arenosa sp. nov., isolated
from marine sand. Int. J. Syst. Evol. Microbiol. 66, 5514–5518. doi: 10.1099/ijsem. Schöttner, S., Pfitzner, B., Grünke, S., Rasheed, M., Wild, C., and Ramette,
0.001549 A. (2011). Drivers of bacterial diversity dynamics in permeable carbonate and

silicate coral reef sands from the Red Sea. Environ. Microbiol. 13, 1815–1826. Thode-Andersen, S., and Jørgensen, B. B. (1989). Sulfate reduction and the
doi: 10.1111/j.1462-2920.2011.02494.x formation of 35S-labeled FeS, FeS2, and S0 in coastal marine sediments. Limnol.
Oceanogr. 34, 793–806. doi: 10.4319/lo.1989.34.5.0793
Serrano, R., Gras, L., Giménez-Casalduero, F., Del-Pilar-Ruso, Y., Grindlay, G.,
and Mora, J. (2019). The role of Cymodocea nodosa on the dynamics of trace Toes, A. C. M., Finke, N., Kuenen, J. G., and Muyzer, G. (2008). Effects
elements in different marine environmental compartments at the Mar Menor of deposition of heavy-metal-polluted harbor mud on microbial diversity and
Lagoon (Spain). Mar. Pollut. Bull. 141, 52–60. doi: 10.1016/j.marpolbul.2019.02. metal resistance in sandy marine sediments. Arch. Environ. Contam. Toxicol. 55,
019 372–385. doi: 10.1007/s00244-008-9135-4
Sharifuzzaman, S. M., Rahman, H., Ashekuzzaman, S. M., Islam, M. M., Torti, A., Jørgensen, B. B., and Lever, M. A. (2018). Preservation of microbial
Chowdhury, S. R., and Hossain, M. S. (2016). “Heavy metals accumulation DNA in marine sediments: Insights from extracellular DNA pools. Environ.
in coastal sediments,” in Environmental Remediation technologies for metal- Microbiol. 20, 4526–4542. doi: 10.1111/1462-2920.14401
contaminated soils, eds H. Hasegawa I, M. M. Rahman, and M. A. Rahman (Tokyo:
Springer), 21–42. doi: 10.1007/978-4-431-55759-3_2 Treude, N., Rosencrantz, D., Liesack, W., and Schnell, S. (2003). Strain FAc12,
a dissimilatory iron-reducing member of the Anaeromyxobacter subgroup of
Simonneau, J. (1973). Mar menor: Evolution sedimentologique et geoquimique Myxococcales. FEMS Microbiol. Ecol. 44, 261–269. doi: 10.1016/S0168-6496(03)
recente du remplissage. Toulouse: Université Paul Sebatier of Tolouse. 00048-5
Sipos, R., Székely, A. J., Palatinszky, M., Révész, S., Márialigeti, K., and Ugarelli, K., Chakrabarti, S., Laas, P., and Stingl, U. (2017). The
Nikolausz, M. (2007). Effect of primer mismatch, annealing temperature and PCR seagrass holobiont and its microbiome. Microorganisms 5:81. doi:
cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS 10.3390/microorganisms5040081
Microbiol. Ecol. 60, 341–350. doi: 10.1111/j.1574-6941.2007.00283.x
Ugarelli, K., Laas, P., and Stingl, U. (2019). The microbial communities of leaves
Soergel, D. A. W., Dey, N., Knight, R., and Brenner, S. E. (2012). Selection of and roots associated with turtle grass (Thalassia testudinum) and manatee grass
primers for optimal taxonomic classification of environmental 16S rRNA gene (Syringodium filliforme) are distinct from seawater and sediment communities,
sequences. ISME J. 6, 1440–1444. doi: 10.1038/ismej.2011.208 but are similar between species and sampling sites. Microorganisms 7:4. doi: 10.
Sørensen, J., Jørgensen, B. B., and Revsbech, N. P. (1979). A comparison of 3390/microorganisms7010004
oxygen, nitrate, and sulfate respiration in coastal marine sediments. Microb. Ecol.
5, 105–115. doi: 10.1007/BF02010501 Urich, T., Lanzén, A., Stokke, R., Pedersen, R. B., Bayer, C., Thorseth,
I. H., et al. (2014). Microbial community structure and functioning in marine
Sørensen, K. B., Glazer, B., Hannides, A., and Gaidos, E. (2007). Spatial structure sediments associated with diffuse hydrothermal venting assessed by integrated
of the microbial community in sandy carbonate sediment. Mar. Ecol. Prog. Ser. meta-omics. Environ. Microbiol. 16, 2699–2710. doi: 10.1111/1462-2920.
346, 61–74. doi: 10.3354/meps06996 12283
Sorokin, D. Y., Merkel, A. Y., and Muyzer, G. (2020). “Thiohalophilus,” in Vandieken, V., Mußmann, M., Niemann, H., and Jørgensen, B. B. (2006).
Bergey’s manual of systematics of archaea and bacteria, ed. W. B. Whitman Desulfuromonas svalbardensis sp. nov. and Desulfuromusa ferrireducens sp. nov.,
(Hoboken, NJ: John Wiley & Sons), 1–7. doi: 10.1002/9781118960608.gbm01693 psychrophilic, Fe(III)-reducing bacteria isolated from Arctic sediments, Svalbard.
Straub, D., Blackwell, N., Langarica-Fuentes, A., Peltzer, A., Nahnsen, S., and Int. J. Syst. Evol. Microbiol. 56, 1133–1139. doi: 10.1099/ijs.0.63639-0
Kleindienst, S. (2020). Interpretations of environmental microbial community Vepraskas, M. J., and Faulkner, S. P. (2001). Redox chemistry of hydric soils. Boca
studies are biased by the selected 16S rRNA (gene) amplicon sequencing pipeline. Raton, FL: Lewis.
Front. Microbiol. 11:550420. doi: 10.3389/fmicb.2020.550420
Wickham, H. (2016). ggplot2: Elegant graphics for data analysis. New York, NY:
Suárez-Suárez, A., López-López, A., Tovar-Sánchez, A., Yarza, P., Orfila, A., Springer-Verlag.
Terrados, J., et al. (2011). Response of sulfate-reducing bacteria to an artificial
oil-spill in a coastal marine sediment. Environ. Microbiol. 13, 1488–1499. doi: Williams, T. A., Cox, C. J., Foster, P. G., Szöllõsi, G. J., and Embley, T. M. (2020).
10.1111/j.1462-2920.2011.02451.x Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol.
Evol. 4, 138–147. doi: 10.1038/s41559-020-01347-2
Sun, M. Y., Dafforn, K. A., Johnston, E. L., and Brown, M. V. (2013). Core
sediment bacteria drive community response to anthropogenic contamination Wu, S., Li, R., Xie, S., and Shi, C. (2019). Depth-related change of sulfate-
over multiple environmental gradients. Environ. Microbiol. 15, 2517–2531. doi: reducing bacteria community in mangrove sediments: The influence of heavy
10.1111/1462-2920.12133 metal contamination. Mar. Pollut. Bull. 140, 443–450. doi: 10.1016/j.marpolbul.
2019.01.042
Sun, S., Jones, R. B., and Fodor, A. A. (2020). Inference-based accuracy of
metagenome prediction tools varies across sample types and functional categories. Xing, L., Zhang, W., Gu, M., Yin, Q., and Wu, G. (2020). Microbial interactions
Microbiome 8, 1–9. doi: 10.1186/s40168-020-00815-y regulated by the dosage of ferroferric oxide in the co-metabolism of organic carbon
and sulfate. Bioresour. Technol. 296:122317. doi: 10.1016/j.biortech.2019.122317
Suzuki, M., Rappé, M. S., and Giovannoni, S. J. (1998). Kinetic bias in estimates
of coastal picoplankton community structure obtained by measurements of small- Yamada, T., and Sekiguchi, Y. (2015). “Anaerolineaceae,” in Bergey’s manual of
subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. systematics of archaea and bacteria, eds W. B. Whitman, F. Rainey, P. Kämpfer, M.
64, 4522–4529. doi: 10.1128/aem.64.11.4522-4529.1998 Trujillo, J. Chun, P. DeVos, B. Hedlund, and S. Dedysh (Hoboken, NJ: John Wiley
& Sons), 1–5. doi: 10.1002/9781118960608.fbm00301
Takahashi, S., Tomita, J., Nishioka, K., Hisada, T., and Nishijima, M. (2014).
Development of a prokaryotic universal primer for simultaneous analysis of Zaremba-Niedzwiedzka, K., Caceres, E. F., Saw, J. H., Bäckström, D., Juzokaite,
Bacteria and Archaea using next-generation sequencing. PLoS One 9:e105592. L., Vancaester, E., et al. (2017). Asgard archaea illuminate the origin of eukaryotic
doi: 10.1371/journal.pone.0105592 cellular complexity. Nature 541, 353–358. doi: 10.1038/nature21031
Terrados, J., and Ros, J. (1991). Production dynamics in a macrophyte- Zhang, Y., Ma, Y., Zhang, R., Zhang, B., Zhai, X., Li, W., et al. (2019).
dominated ecosystem: The Mar Menor coastal lagoon (SE Spain). Oecologia Aquat. Metagenomic resolution of functional diversity in copper surface-associated
10, 255–270. marine biofilms. Front. Microbiol. 10:2863. doi: 10.3389/fmicb.2019.02863
Terrados, J., and Ros, J. D. (1992). Growth and primary production of Zhong, S., Khodursky, A., Dykhuizen, D. E., and Dean, A. M. (2004).
Cymodocea nodosa (Ucria) Ascherson in a Mediterranean coastal lagoon: The Mar Evolutionary genomics of ecological specialization. Proc. Natl. Acad. Sci. U.S.A.
Menor (SE Spain). Aquat. Bot. 43, 63–74. doi: 10.1016/0304-3770(92)90014-A 101, 11719–11724. doi: 10.1073/pnas.0404397101

Factors Structuring Microbial Communities in Highl

Uploaded by

Copyright:

Available Formats

Factors Structuring Microbial Communities in Highl

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Factors Structuring Microbial Communities in Highl

Uploaded by

Copyright:

Available Formats

TYPE Original Research

PUBLISHED 07 September 2022

Factors structuring microbial

Frontiers in Microbiology 01 frontiersin.org

than those in the non-contaminated stations. This finding suggests that

Introduction by several anthropogenic factors (Marín-Guirao et al., 2005;

Frontiers in Microbiology 02 frontiersin.org

Frontiers in Microbiology 03 frontiersin.org

Frontiers in Microbiology 04 frontiersin.org

Frontiers in Microbiology 05 frontiersin.org

General characteristics of the

Frontiers in Microbiology 06 frontiersin.org

Frontiers in Microbiology 07 frontiersin.org

Frontiers in Microbiology 08 frontiersin.org

Frontiers in Microbiology 09 frontiersin.org

Frontiers in Microbiology 10 frontiersin.org

Frontiers in Microbiology 11 frontiersin.org

Frontiers in Microbiology 12 frontiersin.org

Significant OTUs PTE samples vs. time (%)

OTUs contributing to changes in PTE

Frontiers in Microbiology 13 frontiersin.org

Frontiers in Microbiology 14 frontiersin.org

Frontiers in Microbiology 15 frontiersin.org

Frontiers in Microbiology 16 frontiersin.org

Frontiers in Microbiology 17 frontiersin.org

Frontiers in Microbiology 18 frontiersin.org

You might also like