This study shows that Vochysia guatemalensis tree plantations were associated with enhanced soil ... more This study shows that Vochysia guatemalensis tree plantations were associated with enhanced soil biotic and abiotic characteristics in previously cleared forests in the Northern Zone of Costa Rica, suggesting the possible use of this practice as a restoration strategy for local land owners. Soil samples from a primary forest (PF), secondary forest (SF), and a 13-year-old (OV) plantation of V. guatemalensis had greater relative abundances of DNA sequences of microbial genera critical for C-use efficiency (i.e., the saprobe, complex C and wood rot/lignin decomposer fungi, and bacterial lignin and other complex C degraders), and greater levels of total organic C, C-biomass, and Microbial Quotients as indicators of enhanced C-use efficiency, than found in soils of adjacent 5-year-old (NV) V. guatemalensis plantations and abandoned non-productive pasture/grasslands (GR). The major research conclusions were that: 1) conversion of forested land into abandoned pasture/grasslands decreased the C-use efficiency in the soils and the microbial groups associated with C-use efficiency; 2) soils in plantations of V. guatemalensis were associated with increased abundances of the DNA of these same microbial groups and enhanced C-use efficiency; 3) DNA-based taxonomic analysis of microbes and analysis of the Microbial Quotient values can be used to monitor soil ecosystems for assessment of the efficacy of restoration activities. Thus, planting V. guatemalensis on damaged lands in the Maquenque National Wildlife Refuge (MNWR) should be encouraged to provide a sustainable forestry crop that can be harvested rotationally, while improving soil ecosystem health and reducing the pressure to harvest other forest sites.
The long-term effects of reforestation versus maintained grassland on microbial community structu... more The long-term effects of reforestation versus maintained grassland on microbial community structure and nutrient cycling provide a valuable perspective on ecosystem health and carbon sequestration potential of tropical soils in the heavily deforested Northern Zone of Costa Rica. The soil from the secondary forests in this area had greater levels of phosphate, inorganic nitrogen, organic carbon, respiratory activity, abundance and diversity of Basidomycete rDNA, abundance of fungal rDNA, and lower abundance but greater diversity of Rhizobium rDNA, and less abundance of nifH gene DNA than soils from adjacent grasslands of the same age. Critical correlations were observed between the abundance of Basidiomycete rDNA and laccase gene with the levels of phosphate, microbial biomass, organic carbon use efficiency, and percent water saturation. These data suggest a trend towards the secondary forest soils becoming more fungal-dominant, with greater microbial activity, greater nitrogen mineralization activity and more efficient use of carbon. This project provides some of the first evidence that the management strategy of regeneration of secondary forests results in more complex soil ecosystems, with greater potential for carbon sequestration than the maintained grasslands.
In Costa Rica, the Maquenque National Wildlife Refuge (MNWLR) contains a unique habitat gradient ... more In Costa Rica, the Maquenque National Wildlife Refuge (MNWLR) contains a unique habitat gradient ranging from primary old growth forests, grasslands, pastures, to various ages of secondary forests. Within these primary old growth forests are extremely dense naturally occurring Bromelia pinguin (Bromeliaceae) patches that often grow with densities up to 2 plants per square meter. A previous study found that anti-fungal activity of this particular plant appears to be altering the fungal community in soils adjacent to these plants. No work has been previously conducted on the possible effects of this plant community on soil faunal communities and if seasonality contributes to changes in soil invertebrate populations along a moisture gradient. Thus, a study was conducted to assess the effects of this specialized plant community on soil invertebrates with respect to season, and if these changes in soil fauna guild structure could prove to be valid candidates as indicators of ecosystem condition with changes in precipitation. In addition, a meta-analysis was done to determine how the bromeliadassociated soil invertebrate communities differ from those in adjacent primary forest soils. Therefore, comparisons were determined from previous primary forest soil invertebrate environmental DNA (eDNA) to the current wet season bromeliad soil invertebrate eDNA. Roche 454 pyro-sequencing was conducted on the 650 bp fragment of the cytochrome oxidase subunit I (COI) gene of invertebrates to obtain and characterize soil invertebrate sequence composition. To determine relationships among soil fauna guilds across seasons, relative abundance of the sequences were calculated, and used in conjunction with EcoSim niche overlap and co-occurrence values. From the bromeliad seasonal soil fauna eDNA study, it appears certain invertebrate guilds are driven by moisture as indicated by fluctuations in relative abundance of each invertebrate guild across seasons in bromeliad patch soils, as well as indicated by EcoSim niche overlap values. In particular, Guilds 1, 4, and 5, should warrant further investigation as indicators of habitat condition. The meta-analysis showed that a naturally occurring modified environment (the bromeliad patches), can result in differences in relative abundance and partitioning of a limited resource between invertebrate guild structure. Those guilds associated with microbivorous and complex decomposition activities (i.e. Guilds 3 and 4), are more abundant in primary forest soils than bromeliad patch soils and could potentially used for bioindicators of habitat perturbations.
Aims Legacy attributes from land-use history have lingering effects on soil and its below-ground ... more Aims Legacy attributes from land-use history have lingering effects on soil and its below-ground components undergoing succession that has important consequences for regenerating tropical secondary forests. Yet, even landscapes of similar origins with analogous land-use histories have exhibited differing routes of forest recovery with different outcomes. There is increasing evidence that tree species-generated soil microbial heterogeneity is an important factor in facilitating regeneration, particularly nitrogen (N)-fixing tree species. However, it is unclear how land-use history influences the soil microbiome of important N-fixing plants developing under these conditions; at different life stages of Nfixing plant development; and how this compares to a primary forest. Methods We examined differences in composition of the soil bacterial and fungal communities and their determinants (i.e. soil environmental factors) associated with large-, medium-, and small-sized Pentaclethra macroloba trees in a primary forest and in a 23-yearold secondary forest with contrasting land-use histories. Results We show that as Pentaclethra increases in size (and/or age), the soil microbiome associated with Pentaclethra also changes, and that these soil microbiomes can become similar even when developed in soils of contrasting land-use histories. We found that soil NH 4 + and NO 3 − explained 61% of the variation in the soil bacterial community composition of small trees between the primary and secondary forest. Conclusions This highlights the importance of inorganic N during tree soil microbiome development in contrasting land-use history of soils. Our findings suggest that legacy effects on may be mediated through size (and/or age) of Pentaclethra and its associated soil microbiome.
It is now widely accepted that the majority of tropical landscapes are in transition from disturb... more It is now widely accepted that the majority of tropical landscapes are in transition from disturbance to recovery. Remediation efforts are occurring in Central and South America, attempting to recuperate the soils, often using indigenous nitrogen (N)-fixing tree species. Tree species-generated soil microbial heterogeneity might be important in facilitating regeneration of forest vegetation growth and, although some work has identified these efforts may enhance the soil carbon (C), there have been few studies conducted on how these trees are affecting the below-ground soil biological dynamics in these regions. Here, we explored how and to what extent individual plant effects of a native N-fixing and non-N-fixing plant has affected the below-ground soil C and N metrics and soil bacterial and fungal community composition. To begin to address this, we examined if there were differences in various soil abiotic factors (ToC, TN, C:N ratio, C mic , NH 4 + , NO 3 − , pH, and % moisture) and in the soil bacterial and fungal community composition associated with soil of a native non-N-fixer, Dipteryx panamensis and a native N-fixer, Pentaclethra macroloba, and in comparison to the primary forest bulk-soil in which these tree species occur. We found that primary forest-soils had the greatest amounts of soil NH 4 + and C mic , followed by Pentaclethra-soils. Dipteryx-soils had the least amount of soil C mic and NH 4 + , but the greatest amounts of soil NO 3 −. The PERMANOVA results indicated that the Bray-Curtis soil bacterial and fungal community compositions were significantly different between N-fixing and non-N-fixing tree-soils, and also to that of the primary forest-soils. Our results also demonstrated that soil NH 4 + best explained the variation observed in the soil C mic patterns (39.2%), and, both the soil bacterial (22.8%) and fungal community composition (18.1%). Furthermore, we provide evidence that the N-fixer Pentaclethra-soils stimulates the production of more soil C mic than the non-N-fixer Dipteryx-soils. It is clear that these tree species are important in creating changes in the soil microbial community composition, and that NH 4 + may be associated with a shift in a functional response that may have implications for CUE and remediation in this region. et al., 2015). As soil microbes are key components in biogeochemical and nutrient cycling processes, it is thought that tree species-generated soil microbial heterogeneity may be an important factor in facilitating forest regeneration, and thus, critical to the recovery of tropical forests following disturbance. Following forest clearing, N-fixing plants with N-fixing microbial root nodule symbionts are considered to be the principal pathway that disturbed forests recuperate N (Eaton et al., 2012; Shebitz and Eaton, 2013). Indeed, remediation attempts throughout Costa Rica have been
Bacteria in the genus Rhizobium, methanogenic bacteria and Archaea are important in the terrestri... more Bacteria in the genus Rhizobium, methanogenic bacteria and Archaea are important in the terrestrial carbon (C) and nitrogen (N) cycle dynamics and the sequestration of C and N into the soil biomass. A better understanding of the functions of these microbial groups could provide some clarity on the impact of different land development practices and a changing climate on soil ecosystems. The community structure of these three groups of soil microbes was compared between a secondary forest and a forest dominated by the leguminous tree Pentaclethra macroloba within a Costa Rican rainforest. The secondary forest soils had a greater total microbial biomass and efficiency of C utilization, greater relative abundance of methanotrophs and Archaea 16s rDNA, and greater overall microbial diversity, whereas the relative abundance of Rhizobium was greater in the Pentaclethra macroloba-dominant forest soil. The data suggest that rhizobia, methanotrophs and Archaea are involved in a complex interplay that affects the C and N cycle dynamics.
In the current study, we showed that Pentaclethra macroloba appears to influence the microbial co... more In the current study, we showed that Pentaclethra macroloba appears to influence the microbial communities within the soil of secondary forests in the Northern Zone of Costa Rica. The soil closest to the Pentaclethra macroloba trees ("tree soil") had a lower abundance of the N-fixing bacteria Frankia, but greater amounts of both nifH gene and Rhizobium than soils furthest away ("forest soils"). These soils also had greater amounts of microbial biomass and were more efficient at organic carbon use as indicated by lower metabolic quotient values (qCO2). This suggests that the use of Pentaclethra macroloba in restoration of soils from harvested forests may provide a good strategy for recuperating nitrogen in the soils due to its association with N-fixing bacteria near the roots of the trees and in the nearby soils. As well, these trees were associated with enhanced microbial biomass, microbial activity, and microbial mediated enhanced efficiency of C use into the biomass, suggesting their value in improving soil richness. A tangential discovery during this study was that it was the first, to our knowledge to show the presence of Frankia in association with Pentaclethra macroloba. It is interesting to note that significant amounts of Frankia were found throughout the soils in this study, and it was present in all sites at levels far greater than Rhizobium. It is likely that Frankia is more critical in recuperating soil N within these developing secondary forests.
Your article is protected by copyright and all rights are held exclusively by Springer Science +B... more Your article is protected by copyright and all rights are held exclusively by Springer Science +Business Media New York. This e-offprint is for personal use only and shall not be selfarchived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com".
The soil microbial community is not only critical to nutrient recycling and mineralization of org... more The soil microbial community is not only critical to nutrient recycling and mineralization of organic material, but also plays a fundamental role in influencing plant community composition (
Severe liver disease was associated with mortality in Atlantic salmon Salmo salar maintained in s... more Severe liver disease was associated with mortality in Atlantic salmon Salmo salar maintained in seawater net pens in Port Townsend Bay, Washington, USA. Approximately 2 mo after seawater introduction prominent diffuse hydropic degeneration and pyknosis of hepatocytes were observed in moribund fish. As the disease progressed, the livers of affected fish exhibited multifocal areas of regenerating hepatocytes intermixed throughout a necrotic parenchyma. Nuclear pleomorphism, karyomegaly and hepatic megalocytosis were prominent in fish surviving at 6 mo post seawater introduction, and many of the enlarged hepatocytes exhibited nuclear inclusions which arose from cytoplasmic invaginations. The lesions were consistent with toxicopathic changes; bacterial and viral examinations revealed no infectious agent associated with the liver damage. The source of the suspected toxicant was most likely direct water contact or natural food rather than the commercial feed because the liver lesions were not detected in Atlantic salmon fed the same commercial diet but reared at a different seawater location (Port Angeles, Washington). Furthermore, fish at both locations originated from the same freshwater hatchery and were of the same genetic strains. Cumulative mortalities at the Port Townsend sites were over 90 %, attributed primarily to the liver lesions. However, some moribund fish also had idiopathic pancreatitis; Aeromonas salmonicida, Cytophaga-Flexibacter and sea lice Lepeophtheirus salmonis mfections; others were lost to seal predation.
A virus (SGV) was isolated from sand goby Oxyeleotris marrnoratus with ulcer disease reared in fr... more A virus (SGV) was isolated from sand goby Oxyeleotris marrnoratus with ulcer disease reared in freshwater cages in Thailand. The virus was typical of members of the aquatic birnaviruses but it possessed phenotypic, serological and biochemical properties that distinguished it from previously described viruses of the Bimaviridae. Serologically, the virus is distinct from the described strains of infectious pancreatic necrosis virus (IPNV) and possesses the capability of replicating in several cell lines from warm water fishes at 30 'C. The use of rapid double-stranded RNA analyses and the immunoprecipltation of radio-labeled virion polypeptides demonstrated the unique biochemical nature of SGV and established the value of these techniques for strain identification of birnaviruses.
Abstract Logging road development is considered as potentially more damaging to a tropical forest... more Abstract Logging road development is considered as potentially more damaging to a tropical forest than the felling of the actual trees. However, little work has been conducted to determine how logging road development impacts the soil microbial communities and associated C and N cycle activities in tropical forests. This study was conducted within an upland tropical forest in the Northern Zone of Costa Rica that had a 2-year abandoned logging road system (used for harvesting trees felled during a tornado) to determine how development of logging roads affected soil C and N cycle activities, efficiency of organic C use, and bacterial and fungal community compositions. Soil samples from a set of logging roads, the road edges, and adjacent primary forests were analyzed for C, N metrics, the Microbial Quotients, and DNA-based microbial taxonomic community compositions; which were tested for differences using multivariate statistical analyses. The logging road soils had significantly greater bulk density and clay, and lower levels of sand, TN, NO3−, NO3−/NH4+, TOC, C Biomass, and Microbial Quotients compared to the road edge and forest soils. The composition of the total bacterial genera of the road edge and forest soils were similar to one another and different from that of the logging road soils, and the composition of the total fungal genera was unique within each of the three areas sampled. The relative abundance of DNA sequences of N-cycle bacteria were greater, and lignin degrading bacteria and wood rot/lignin degrading fungi were less in the logging roads compared to the edge and forest soils. These results suggest that the rate of recovery of both the C and N cycle activities and associated microbial groups in the soils from the road edges is occurring more rapidly than in the abandoned logging road soils. Thus, we suggest that a new tropical forest management practice should include the movement of the slash and debris from the road edge regions onto the logging roads after abandonment, as it would enhance the rate of recovery of both the C and N cycle activities in the soils, and perhaps begin to address the concern that logging roads add an additional 10–15 years to tropical forest recovery following deforestation.
Inga edulis and Pentaclethra macroloba are dominant N-fixing forest trees in Costa Rica, likely i... more Inga edulis and Pentaclethra macroloba are dominant N-fixing forest trees in Costa Rica, likely important for recovery of soil N and C after deforestation, yet little is known of their soil microbiomes nor how land use impacts them. Soils from both trees in a primary and secondary forest were assessed for N-cycle metrics and DNA sequence-based composition of total bacterial, potential N-fixing bacterial, and potential ammonium oxidizing bacterial genera. The compositions of the functional groups of bacteria, but not their total relative abundance of DNA, were different across the soils. The P. macroloba soils had greater NO3− levels and richness of both functional groups, while I. edulis soils had greater NH4+ levels, consistent with its NH4+ preference for root nodule development. The bacterial communities were different by habitat, as secondary forest I. edulis microbiomes were less rich, more dominant, possibly more affected by the disturbance, or reached equilibrium status quick...
The goals of the research presented in this issue of Tropical Ecology were to demonstrate that di... more The goals of the research presented in this issue of Tropical Ecology were to demonstrate that differences in soil DNA-based microbial community characteristics, biomass, microbial activity, and C and N nutrient dynamics can be used as indicators of environmental change, specifically to show how land management, restoration strategies and climate change may be impacting the soil ecosystems of lowland forests and montane cloud forests of Costa Rica. In the studies conducted in lowland secondary forests, the bacterium Frankia was found to be critical for nitrogen-fixation in the soils associated with nitrogen-fixing tree Pentaclethra macroloba, but Frankia, Rhizobium, Archaea, and Type II methanotrophs were also collectively important in recuperation of the soil N and in enhancing microbial biomass C via more efficient use of organic C. These same secondary forest soils had greater levels of inorganic P and N, organic carbon, and microbial activity, and were more fungal-dominant soil ...
Little is known of how hurricane-induced deposition of canopy material onto tropical forest floor... more Little is known of how hurricane-induced deposition of canopy material onto tropical forest floors influences the soil microbial communities involved in decomposition of these materials. In this study, to identify how soil bacterial and fungal communities might change after a hurricane, and their possible roles in the C and N cycles, soils were collected from five 2000 m 2 permanent plots in Lowland, Upland and Riparian primary forests in Costa Rica 3 months before and 7 months after Hurricane Otto damaged the forests. The soil Water, inorganic N and Biomass C increased and total organic C decreased Post-Hurricane, all of which best predicted the changes in the Post-Hurricane soil microbial communities. Post-Hurricane soils from all forest types showed significant changes in community composition of total bacteria, total fungi, and five functional groups of microbes (i.e., degrading/lignin degrading, NH 4 +-producing, and ammonium oxidizing bacteria, and the complex C degrading/wood rot/ lignin degrading and ectomycorrhizal fungi), along with a decrease in richness in genera of all groups. As well, the mean proportion of DNA sequences (MPS) of all five functional groups increased. There were also significant changes in the MPS values of 7 different fungal and 7 different bacterial genera that were part of these functional groups. This is the first evidence that hurricane-induced deposition of canopy material is stimulating changes in the soil microbial communities after the hurricane, involving changes in specific taxonomic and functional group genera, and reduction in the community richness while selecting for dominant genera possibly better suited to process the canopy material. These changes may represent examples of taxonomic switching of functionally redundant microbial genera in response to dramatic changes in resource input. It is possible that differences in these microbial communities and genera may serve as indicators of disturbed and recovering regional soil ecosystems, and should be evaluated in the future.
Hurricanes rapidly deposit large amounts of canopy material onto tropical forest floors, stimulat... more Hurricanes rapidly deposit large amounts of canopy material onto tropical forest floors, stimulating metabolic processes involved in the decomposition of these materials and production of N and C resources into the food web. However, little is known about the effects that hurricanes have on specific soil microbial taxa or functional groups involved in these processes. The objectives of this study were to determine how Hurricane Otto influenced three different tropical forest soil ecosystems within the first 8 months after causing damage to a tropical forest by assessing the soil C and N factors and how the soil bacterial and fungal community compositions differed before and after the hurricane. Soil samples were collected from five 2000 m 2 permanent plots in Lowland, Upland and Riparian forest systems within the same area in the Northern Zone of Costa Rica. Standard methods were used to measure the amounts Total N, NO 3-, NH 4 + , Total organic C, and Biomass C, while Illumina MiSeq methods were used to generate bacterial and fungal sequences. All data were analyzed using univariate and multivariate statistical methods. Using this "before and after" study design, it was found that the levels of the inorganic N and Biomass C were greater in the Post-Hurricane soil samples. The mean proportion of DNA sequences of complex C degrading/lignin degrading, NH 4 +-producing, and ammonium oxidizing bacteria, and the complex C degrading/wood rot/lignin degrading and ectomycorrhizal fungi also were greater in the Post-Hurricane soils. We also provide evidence that the excessive amounts of canopy leaf litter and woody debris deposited on the forest floor during Hurricane Otto appears to be selecting for genera that become more dominant Post-Hurricane, perhaps because they may be better able to rapidly process the newly deposited C and .
Through a grant from the National Science Foundation's Research Experiences for Undergraduates (N... more Through a grant from the National Science Foundation's Research Experiences for Undergraduates (NSF REU), 24 undergraduates (more than half from underrepresented demographic groups) addressed ecological and natural resource management questions within the Maquenque National Wildlife Refuge between 2013 and 2015. Students worked with faculty mentors and researched vegetation, invertebrates, primates, soil microbial community structures, or soil biogeochemical characteristics within a variety of undamaged, damaged, or at-risk habitats. This article highlights some studies conducted by students that sought to provide new ecological information to Costa Rica's Research and Monitoring Plan. Development and diversity are compared within a variety of sites, including selectively harvested forests, 10-to 30-year-old regenerating secondary forests, silviculture plots, and recent agriculture sites that were left fallow. Outcomes in student learning, scientific growth, and ability to connect personal research to that of others are presented. The research experience encouraged the students to become scientists with a global perspective in ecology and environmental sciences, and provided data that can be used for future land management and educational purposes.
Tropical secondary forests currently represent over half of the world's remaining tropical fo... more Tropical secondary forests currently represent over half of the world's remaining tropical forests and are critical candidates for maintaining global biodiversity and enhancing potential carbon-use efficiency (CUE) and, thus, carbon sequestration. However, these ecosystems can exhibit multiple successional pathways, which have hindered our understanding of the soil microbial drivers that facilitate improved CUE. To begin to address this, we examined soil % C; % N; C:N ratio; soil microbial biomass C (C); NO; NH; pH; % moisture; % sand, silt, and clay; and elevation, along with soil bacterial and fungal community composition, and determined which soil abiotic properties structure the soil C and the soil bacterial and fungal communities across a primary forest, 33-year-old secondary forest, and 22-year-old young secondary in the Northern Zone of Costa Rica. We provide evidence that soil microbial communities were mostly distinct across the habitat types and that these habitats app...
A plasmacytoid leukemia (PL) has caused mortalities in chinook salmon (Oncorhynchus tshawytscha) ... more A plasmacytoid leukemia (PL) has caused mortalities in chinook salmon (Oncorhynchus tshawytscha) reared in seawater netpens in western British Columbia, Canada, since 1988. Kidney or eye tissues from 11 of 13 fish from netpens with clinical PL had reverse transcriptase (RT) activity. This RT activity was associated with virus particles of retrovirus morphology and buoyant density. In a transmission experiment, PL-positive donor fish tissues also had RT activity and virus particles of retrovirus morphology and buoyant density, as did recipient fish tissues following development of the disease 6 weeks postinjection with a tissue homogenate from the donor fish. Kidney and spleen tissues from fish that developed PL following injection with an inoculum that was passed through a 0.22-micron filter, in a separate experiment (M. L. Kent and S. C. Dawe. Further evidence for a viral etiology in the plasmacytoid leukemia of chinook salmon Oncorhynchus tshawytscha. Dis. Aquat. Org., in press, 1...
This study shows that Vochysia guatemalensis tree plantations were associated with enhanced soil ... more This study shows that Vochysia guatemalensis tree plantations were associated with enhanced soil biotic and abiotic characteristics in previously cleared forests in the Northern Zone of Costa Rica, suggesting the possible use of this practice as a restoration strategy for local land owners. Soil samples from a primary forest (PF), secondary forest (SF), and a 13-year-old (OV) plantation of V. guatemalensis had greater relative abundances of DNA sequences of microbial genera critical for C-use efficiency (i.e., the saprobe, complex C and wood rot/lignin decomposer fungi, and bacterial lignin and other complex C degraders), and greater levels of total organic C, C-biomass, and Microbial Quotients as indicators of enhanced C-use efficiency, than found in soils of adjacent 5-year-old (NV) V. guatemalensis plantations and abandoned non-productive pasture/grasslands (GR). The major research conclusions were that: 1) conversion of forested land into abandoned pasture/grasslands decreased the C-use efficiency in the soils and the microbial groups associated with C-use efficiency; 2) soils in plantations of V. guatemalensis were associated with increased abundances of the DNA of these same microbial groups and enhanced C-use efficiency; 3) DNA-based taxonomic analysis of microbes and analysis of the Microbial Quotient values can be used to monitor soil ecosystems for assessment of the efficacy of restoration activities. Thus, planting V. guatemalensis on damaged lands in the Maquenque National Wildlife Refuge (MNWR) should be encouraged to provide a sustainable forestry crop that can be harvested rotationally, while improving soil ecosystem health and reducing the pressure to harvest other forest sites.
The long-term effects of reforestation versus maintained grassland on microbial community structu... more The long-term effects of reforestation versus maintained grassland on microbial community structure and nutrient cycling provide a valuable perspective on ecosystem health and carbon sequestration potential of tropical soils in the heavily deforested Northern Zone of Costa Rica. The soil from the secondary forests in this area had greater levels of phosphate, inorganic nitrogen, organic carbon, respiratory activity, abundance and diversity of Basidomycete rDNA, abundance of fungal rDNA, and lower abundance but greater diversity of Rhizobium rDNA, and less abundance of nifH gene DNA than soils from adjacent grasslands of the same age. Critical correlations were observed between the abundance of Basidiomycete rDNA and laccase gene with the levels of phosphate, microbial biomass, organic carbon use efficiency, and percent water saturation. These data suggest a trend towards the secondary forest soils becoming more fungal-dominant, with greater microbial activity, greater nitrogen mineralization activity and more efficient use of carbon. This project provides some of the first evidence that the management strategy of regeneration of secondary forests results in more complex soil ecosystems, with greater potential for carbon sequestration than the maintained grasslands.
In Costa Rica, the Maquenque National Wildlife Refuge (MNWLR) contains a unique habitat gradient ... more In Costa Rica, the Maquenque National Wildlife Refuge (MNWLR) contains a unique habitat gradient ranging from primary old growth forests, grasslands, pastures, to various ages of secondary forests. Within these primary old growth forests are extremely dense naturally occurring Bromelia pinguin (Bromeliaceae) patches that often grow with densities up to 2 plants per square meter. A previous study found that anti-fungal activity of this particular plant appears to be altering the fungal community in soils adjacent to these plants. No work has been previously conducted on the possible effects of this plant community on soil faunal communities and if seasonality contributes to changes in soil invertebrate populations along a moisture gradient. Thus, a study was conducted to assess the effects of this specialized plant community on soil invertebrates with respect to season, and if these changes in soil fauna guild structure could prove to be valid candidates as indicators of ecosystem condition with changes in precipitation. In addition, a meta-analysis was done to determine how the bromeliadassociated soil invertebrate communities differ from those in adjacent primary forest soils. Therefore, comparisons were determined from previous primary forest soil invertebrate environmental DNA (eDNA) to the current wet season bromeliad soil invertebrate eDNA. Roche 454 pyro-sequencing was conducted on the 650 bp fragment of the cytochrome oxidase subunit I (COI) gene of invertebrates to obtain and characterize soil invertebrate sequence composition. To determine relationships among soil fauna guilds across seasons, relative abundance of the sequences were calculated, and used in conjunction with EcoSim niche overlap and co-occurrence values. From the bromeliad seasonal soil fauna eDNA study, it appears certain invertebrate guilds are driven by moisture as indicated by fluctuations in relative abundance of each invertebrate guild across seasons in bromeliad patch soils, as well as indicated by EcoSim niche overlap values. In particular, Guilds 1, 4, and 5, should warrant further investigation as indicators of habitat condition. The meta-analysis showed that a naturally occurring modified environment (the bromeliad patches), can result in differences in relative abundance and partitioning of a limited resource between invertebrate guild structure. Those guilds associated with microbivorous and complex decomposition activities (i.e. Guilds 3 and 4), are more abundant in primary forest soils than bromeliad patch soils and could potentially used for bioindicators of habitat perturbations.
Aims Legacy attributes from land-use history have lingering effects on soil and its below-ground ... more Aims Legacy attributes from land-use history have lingering effects on soil and its below-ground components undergoing succession that has important consequences for regenerating tropical secondary forests. Yet, even landscapes of similar origins with analogous land-use histories have exhibited differing routes of forest recovery with different outcomes. There is increasing evidence that tree species-generated soil microbial heterogeneity is an important factor in facilitating regeneration, particularly nitrogen (N)-fixing tree species. However, it is unclear how land-use history influences the soil microbiome of important N-fixing plants developing under these conditions; at different life stages of Nfixing plant development; and how this compares to a primary forest. Methods We examined differences in composition of the soil bacterial and fungal communities and their determinants (i.e. soil environmental factors) associated with large-, medium-, and small-sized Pentaclethra macroloba trees in a primary forest and in a 23-yearold secondary forest with contrasting land-use histories. Results We show that as Pentaclethra increases in size (and/or age), the soil microbiome associated with Pentaclethra also changes, and that these soil microbiomes can become similar even when developed in soils of contrasting land-use histories. We found that soil NH 4 + and NO 3 − explained 61% of the variation in the soil bacterial community composition of small trees between the primary and secondary forest. Conclusions This highlights the importance of inorganic N during tree soil microbiome development in contrasting land-use history of soils. Our findings suggest that legacy effects on may be mediated through size (and/or age) of Pentaclethra and its associated soil microbiome.
It is now widely accepted that the majority of tropical landscapes are in transition from disturb... more It is now widely accepted that the majority of tropical landscapes are in transition from disturbance to recovery. Remediation efforts are occurring in Central and South America, attempting to recuperate the soils, often using indigenous nitrogen (N)-fixing tree species. Tree species-generated soil microbial heterogeneity might be important in facilitating regeneration of forest vegetation growth and, although some work has identified these efforts may enhance the soil carbon (C), there have been few studies conducted on how these trees are affecting the below-ground soil biological dynamics in these regions. Here, we explored how and to what extent individual plant effects of a native N-fixing and non-N-fixing plant has affected the below-ground soil C and N metrics and soil bacterial and fungal community composition. To begin to address this, we examined if there were differences in various soil abiotic factors (ToC, TN, C:N ratio, C mic , NH 4 + , NO 3 − , pH, and % moisture) and in the soil bacterial and fungal community composition associated with soil of a native non-N-fixer, Dipteryx panamensis and a native N-fixer, Pentaclethra macroloba, and in comparison to the primary forest bulk-soil in which these tree species occur. We found that primary forest-soils had the greatest amounts of soil NH 4 + and C mic , followed by Pentaclethra-soils. Dipteryx-soils had the least amount of soil C mic and NH 4 + , but the greatest amounts of soil NO 3 −. The PERMANOVA results indicated that the Bray-Curtis soil bacterial and fungal community compositions were significantly different between N-fixing and non-N-fixing tree-soils, and also to that of the primary forest-soils. Our results also demonstrated that soil NH 4 + best explained the variation observed in the soil C mic patterns (39.2%), and, both the soil bacterial (22.8%) and fungal community composition (18.1%). Furthermore, we provide evidence that the N-fixer Pentaclethra-soils stimulates the production of more soil C mic than the non-N-fixer Dipteryx-soils. It is clear that these tree species are important in creating changes in the soil microbial community composition, and that NH 4 + may be associated with a shift in a functional response that may have implications for CUE and remediation in this region. et al., 2015). As soil microbes are key components in biogeochemical and nutrient cycling processes, it is thought that tree species-generated soil microbial heterogeneity may be an important factor in facilitating forest regeneration, and thus, critical to the recovery of tropical forests following disturbance. Following forest clearing, N-fixing plants with N-fixing microbial root nodule symbionts are considered to be the principal pathway that disturbed forests recuperate N (Eaton et al., 2012; Shebitz and Eaton, 2013). Indeed, remediation attempts throughout Costa Rica have been
Bacteria in the genus Rhizobium, methanogenic bacteria and Archaea are important in the terrestri... more Bacteria in the genus Rhizobium, methanogenic bacteria and Archaea are important in the terrestrial carbon (C) and nitrogen (N) cycle dynamics and the sequestration of C and N into the soil biomass. A better understanding of the functions of these microbial groups could provide some clarity on the impact of different land development practices and a changing climate on soil ecosystems. The community structure of these three groups of soil microbes was compared between a secondary forest and a forest dominated by the leguminous tree Pentaclethra macroloba within a Costa Rican rainforest. The secondary forest soils had a greater total microbial biomass and efficiency of C utilization, greater relative abundance of methanotrophs and Archaea 16s rDNA, and greater overall microbial diversity, whereas the relative abundance of Rhizobium was greater in the Pentaclethra macroloba-dominant forest soil. The data suggest that rhizobia, methanotrophs and Archaea are involved in a complex interplay that affects the C and N cycle dynamics.
In the current study, we showed that Pentaclethra macroloba appears to influence the microbial co... more In the current study, we showed that Pentaclethra macroloba appears to influence the microbial communities within the soil of secondary forests in the Northern Zone of Costa Rica. The soil closest to the Pentaclethra macroloba trees ("tree soil") had a lower abundance of the N-fixing bacteria Frankia, but greater amounts of both nifH gene and Rhizobium than soils furthest away ("forest soils"). These soils also had greater amounts of microbial biomass and were more efficient at organic carbon use as indicated by lower metabolic quotient values (qCO2). This suggests that the use of Pentaclethra macroloba in restoration of soils from harvested forests may provide a good strategy for recuperating nitrogen in the soils due to its association with N-fixing bacteria near the roots of the trees and in the nearby soils. As well, these trees were associated with enhanced microbial biomass, microbial activity, and microbial mediated enhanced efficiency of C use into the biomass, suggesting their value in improving soil richness. A tangential discovery during this study was that it was the first, to our knowledge to show the presence of Frankia in association with Pentaclethra macroloba. It is interesting to note that significant amounts of Frankia were found throughout the soils in this study, and it was present in all sites at levels far greater than Rhizobium. It is likely that Frankia is more critical in recuperating soil N within these developing secondary forests.
Your article is protected by copyright and all rights are held exclusively by Springer Science +B... more Your article is protected by copyright and all rights are held exclusively by Springer Science +Business Media New York. This e-offprint is for personal use only and shall not be selfarchived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com".
The soil microbial community is not only critical to nutrient recycling and mineralization of org... more The soil microbial community is not only critical to nutrient recycling and mineralization of organic material, but also plays a fundamental role in influencing plant community composition (
Severe liver disease was associated with mortality in Atlantic salmon Salmo salar maintained in s... more Severe liver disease was associated with mortality in Atlantic salmon Salmo salar maintained in seawater net pens in Port Townsend Bay, Washington, USA. Approximately 2 mo after seawater introduction prominent diffuse hydropic degeneration and pyknosis of hepatocytes were observed in moribund fish. As the disease progressed, the livers of affected fish exhibited multifocal areas of regenerating hepatocytes intermixed throughout a necrotic parenchyma. Nuclear pleomorphism, karyomegaly and hepatic megalocytosis were prominent in fish surviving at 6 mo post seawater introduction, and many of the enlarged hepatocytes exhibited nuclear inclusions which arose from cytoplasmic invaginations. The lesions were consistent with toxicopathic changes; bacterial and viral examinations revealed no infectious agent associated with the liver damage. The source of the suspected toxicant was most likely direct water contact or natural food rather than the commercial feed because the liver lesions were not detected in Atlantic salmon fed the same commercial diet but reared at a different seawater location (Port Angeles, Washington). Furthermore, fish at both locations originated from the same freshwater hatchery and were of the same genetic strains. Cumulative mortalities at the Port Townsend sites were over 90 %, attributed primarily to the liver lesions. However, some moribund fish also had idiopathic pancreatitis; Aeromonas salmonicida, Cytophaga-Flexibacter and sea lice Lepeophtheirus salmonis mfections; others were lost to seal predation.
A virus (SGV) was isolated from sand goby Oxyeleotris marrnoratus with ulcer disease reared in fr... more A virus (SGV) was isolated from sand goby Oxyeleotris marrnoratus with ulcer disease reared in freshwater cages in Thailand. The virus was typical of members of the aquatic birnaviruses but it possessed phenotypic, serological and biochemical properties that distinguished it from previously described viruses of the Bimaviridae. Serologically, the virus is distinct from the described strains of infectious pancreatic necrosis virus (IPNV) and possesses the capability of replicating in several cell lines from warm water fishes at 30 'C. The use of rapid double-stranded RNA analyses and the immunoprecipltation of radio-labeled virion polypeptides demonstrated the unique biochemical nature of SGV and established the value of these techniques for strain identification of birnaviruses.
Abstract Logging road development is considered as potentially more damaging to a tropical forest... more Abstract Logging road development is considered as potentially more damaging to a tropical forest than the felling of the actual trees. However, little work has been conducted to determine how logging road development impacts the soil microbial communities and associated C and N cycle activities in tropical forests. This study was conducted within an upland tropical forest in the Northern Zone of Costa Rica that had a 2-year abandoned logging road system (used for harvesting trees felled during a tornado) to determine how development of logging roads affected soil C and N cycle activities, efficiency of organic C use, and bacterial and fungal community compositions. Soil samples from a set of logging roads, the road edges, and adjacent primary forests were analyzed for C, N metrics, the Microbial Quotients, and DNA-based microbial taxonomic community compositions; which were tested for differences using multivariate statistical analyses. The logging road soils had significantly greater bulk density and clay, and lower levels of sand, TN, NO3−, NO3−/NH4+, TOC, C Biomass, and Microbial Quotients compared to the road edge and forest soils. The composition of the total bacterial genera of the road edge and forest soils were similar to one another and different from that of the logging road soils, and the composition of the total fungal genera was unique within each of the three areas sampled. The relative abundance of DNA sequences of N-cycle bacteria were greater, and lignin degrading bacteria and wood rot/lignin degrading fungi were less in the logging roads compared to the edge and forest soils. These results suggest that the rate of recovery of both the C and N cycle activities and associated microbial groups in the soils from the road edges is occurring more rapidly than in the abandoned logging road soils. Thus, we suggest that a new tropical forest management practice should include the movement of the slash and debris from the road edge regions onto the logging roads after abandonment, as it would enhance the rate of recovery of both the C and N cycle activities in the soils, and perhaps begin to address the concern that logging roads add an additional 10–15 years to tropical forest recovery following deforestation.
Inga edulis and Pentaclethra macroloba are dominant N-fixing forest trees in Costa Rica, likely i... more Inga edulis and Pentaclethra macroloba are dominant N-fixing forest trees in Costa Rica, likely important for recovery of soil N and C after deforestation, yet little is known of their soil microbiomes nor how land use impacts them. Soils from both trees in a primary and secondary forest were assessed for N-cycle metrics and DNA sequence-based composition of total bacterial, potential N-fixing bacterial, and potential ammonium oxidizing bacterial genera. The compositions of the functional groups of bacteria, but not their total relative abundance of DNA, were different across the soils. The P. macroloba soils had greater NO3− levels and richness of both functional groups, while I. edulis soils had greater NH4+ levels, consistent with its NH4+ preference for root nodule development. The bacterial communities were different by habitat, as secondary forest I. edulis microbiomes were less rich, more dominant, possibly more affected by the disturbance, or reached equilibrium status quick...
The goals of the research presented in this issue of Tropical Ecology were to demonstrate that di... more The goals of the research presented in this issue of Tropical Ecology were to demonstrate that differences in soil DNA-based microbial community characteristics, biomass, microbial activity, and C and N nutrient dynamics can be used as indicators of environmental change, specifically to show how land management, restoration strategies and climate change may be impacting the soil ecosystems of lowland forests and montane cloud forests of Costa Rica. In the studies conducted in lowland secondary forests, the bacterium Frankia was found to be critical for nitrogen-fixation in the soils associated with nitrogen-fixing tree Pentaclethra macroloba, but Frankia, Rhizobium, Archaea, and Type II methanotrophs were also collectively important in recuperation of the soil N and in enhancing microbial biomass C via more efficient use of organic C. These same secondary forest soils had greater levels of inorganic P and N, organic carbon, and microbial activity, and were more fungal-dominant soil ...
Little is known of how hurricane-induced deposition of canopy material onto tropical forest floor... more Little is known of how hurricane-induced deposition of canopy material onto tropical forest floors influences the soil microbial communities involved in decomposition of these materials. In this study, to identify how soil bacterial and fungal communities might change after a hurricane, and their possible roles in the C and N cycles, soils were collected from five 2000 m 2 permanent plots in Lowland, Upland and Riparian primary forests in Costa Rica 3 months before and 7 months after Hurricane Otto damaged the forests. The soil Water, inorganic N and Biomass C increased and total organic C decreased Post-Hurricane, all of which best predicted the changes in the Post-Hurricane soil microbial communities. Post-Hurricane soils from all forest types showed significant changes in community composition of total bacteria, total fungi, and five functional groups of microbes (i.e., degrading/lignin degrading, NH 4 +-producing, and ammonium oxidizing bacteria, and the complex C degrading/wood rot/ lignin degrading and ectomycorrhizal fungi), along with a decrease in richness in genera of all groups. As well, the mean proportion of DNA sequences (MPS) of all five functional groups increased. There were also significant changes in the MPS values of 7 different fungal and 7 different bacterial genera that were part of these functional groups. This is the first evidence that hurricane-induced deposition of canopy material is stimulating changes in the soil microbial communities after the hurricane, involving changes in specific taxonomic and functional group genera, and reduction in the community richness while selecting for dominant genera possibly better suited to process the canopy material. These changes may represent examples of taxonomic switching of functionally redundant microbial genera in response to dramatic changes in resource input. It is possible that differences in these microbial communities and genera may serve as indicators of disturbed and recovering regional soil ecosystems, and should be evaluated in the future.
Hurricanes rapidly deposit large amounts of canopy material onto tropical forest floors, stimulat... more Hurricanes rapidly deposit large amounts of canopy material onto tropical forest floors, stimulating metabolic processes involved in the decomposition of these materials and production of N and C resources into the food web. However, little is known about the effects that hurricanes have on specific soil microbial taxa or functional groups involved in these processes. The objectives of this study were to determine how Hurricane Otto influenced three different tropical forest soil ecosystems within the first 8 months after causing damage to a tropical forest by assessing the soil C and N factors and how the soil bacterial and fungal community compositions differed before and after the hurricane. Soil samples were collected from five 2000 m 2 permanent plots in Lowland, Upland and Riparian forest systems within the same area in the Northern Zone of Costa Rica. Standard methods were used to measure the amounts Total N, NO 3-, NH 4 + , Total organic C, and Biomass C, while Illumina MiSeq methods were used to generate bacterial and fungal sequences. All data were analyzed using univariate and multivariate statistical methods. Using this "before and after" study design, it was found that the levels of the inorganic N and Biomass C were greater in the Post-Hurricane soil samples. The mean proportion of DNA sequences of complex C degrading/lignin degrading, NH 4 +-producing, and ammonium oxidizing bacteria, and the complex C degrading/wood rot/lignin degrading and ectomycorrhizal fungi also were greater in the Post-Hurricane soils. We also provide evidence that the excessive amounts of canopy leaf litter and woody debris deposited on the forest floor during Hurricane Otto appears to be selecting for genera that become more dominant Post-Hurricane, perhaps because they may be better able to rapidly process the newly deposited C and .
Through a grant from the National Science Foundation's Research Experiences for Undergraduates (N... more Through a grant from the National Science Foundation's Research Experiences for Undergraduates (NSF REU), 24 undergraduates (more than half from underrepresented demographic groups) addressed ecological and natural resource management questions within the Maquenque National Wildlife Refuge between 2013 and 2015. Students worked with faculty mentors and researched vegetation, invertebrates, primates, soil microbial community structures, or soil biogeochemical characteristics within a variety of undamaged, damaged, or at-risk habitats. This article highlights some studies conducted by students that sought to provide new ecological information to Costa Rica's Research and Monitoring Plan. Development and diversity are compared within a variety of sites, including selectively harvested forests, 10-to 30-year-old regenerating secondary forests, silviculture plots, and recent agriculture sites that were left fallow. Outcomes in student learning, scientific growth, and ability to connect personal research to that of others are presented. The research experience encouraged the students to become scientists with a global perspective in ecology and environmental sciences, and provided data that can be used for future land management and educational purposes.
Tropical secondary forests currently represent over half of the world's remaining tropical fo... more Tropical secondary forests currently represent over half of the world's remaining tropical forests and are critical candidates for maintaining global biodiversity and enhancing potential carbon-use efficiency (CUE) and, thus, carbon sequestration. However, these ecosystems can exhibit multiple successional pathways, which have hindered our understanding of the soil microbial drivers that facilitate improved CUE. To begin to address this, we examined soil % C; % N; C:N ratio; soil microbial biomass C (C); NO; NH; pH; % moisture; % sand, silt, and clay; and elevation, along with soil bacterial and fungal community composition, and determined which soil abiotic properties structure the soil C and the soil bacterial and fungal communities across a primary forest, 33-year-old secondary forest, and 22-year-old young secondary in the Northern Zone of Costa Rica. We provide evidence that soil microbial communities were mostly distinct across the habitat types and that these habitats app...
A plasmacytoid leukemia (PL) has caused mortalities in chinook salmon (Oncorhynchus tshawytscha) ... more A plasmacytoid leukemia (PL) has caused mortalities in chinook salmon (Oncorhynchus tshawytscha) reared in seawater netpens in western British Columbia, Canada, since 1988. Kidney or eye tissues from 11 of 13 fish from netpens with clinical PL had reverse transcriptase (RT) activity. This RT activity was associated with virus particles of retrovirus morphology and buoyant density. In a transmission experiment, PL-positive donor fish tissues also had RT activity and virus particles of retrovirus morphology and buoyant density, as did recipient fish tissues following development of the disease 6 weeks postinjection with a tissue homogenate from the donor fish. Kidney and spleen tissues from fish that developed PL following injection with an inoculum that was passed through a 0.22-micron filter, in a separate experiment (M. L. Kent and S. C. Dawe. Further evidence for a viral etiology in the plasmacytoid leukemia of chinook salmon Oncorhynchus tshawytscha. Dis. Aquat. Org., in press, 1...
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