In this study a microbial community suitable for anaerobic digestion of carrot pomace was develop... more In this study a microbial community suitable for anaerobic digestion of carrot pomace was developed from inocula obtained from natural environmental sources. The changes along the process were monitored using pyrosequencing of the 16S rRNA gene. As the community adapted from a diverse natural community to a community with a definite function, diversity decreased drastically. Major bacterial groups remaining after enrichment were Bacilli (31-45.3%), Porphyromonadaceae (12.1-24.8%) and Spirochaetes (12.5-18.5%). The archaeal population was even less diverse and mainly represented by a single OTU that was 99.7% similar to Methanosarcina mazei. One enrichment which failed to produce large amounts of methane had shifts in the bacterial populations and loss of methanogenic archaea.
The American journal of tropical medicine and hygiene, 2004
To describe the midgut microbial diversity and the candidate bacteria for the genetic manipulatio... more To describe the midgut microbial diversity and the candidate bacteria for the genetic manipulation for the generation of transgenic mosquitoes refractory to transmission of diseases, the microbiota of wild Culex quinquefasciatus mosquito midgut was studied using a conventional culture technique and analysis of a 16S ribosomal RNA (rRNA) gene sequence library. The culturable microbiota was identified as Acinetobacter junii, Ac. calcoaceticus, Aeromonas culicicola, Bacillus thuringiensis, Microbacterium oxydans, Pantoea agglomerans, Pseudomonas aeruginosa, Staphylococcus epidermidis, Stenotrophomonas maltophila and an unidentified bacterium from the host Drosophila paulistorium. The 16S rRNA gene library was composed of 46% unidentified and uncultured bacteria, 41% Acinetobacter spp., and 13% Lactococcus spp. The coverage calculated for the 150 clones was 83.3%. Thus, the probability of the next cloned sequence falling in a novel operational taxonomic unit (not yet observed) was 16.7%...
Study of bacterial community dynamics during coconut leaf vermicompost production and in earthwor... more Study of bacterial community dynamics during coconut leaf vermicompost production and in earthworm gut contents using pyrosequencing M. Gopal1,2, K. Jangid2, A. Gupta1,2, W.B. Whitman2, S.R. Prabhu3, G.V. Thomas1 1Microbiology Section, Central Plantation Crops Research Institute, Kasaragod, India, 2Department of Microbiology, University of Georgia, Athens, GA, USA, 3International Bio Recovery Corporation, North Vancouver, BC, Canada Background: Coconut palm (Cocos nucifera L) leaf litter, a recalcitrant waste available in large quantities in India, has been successfully recycled to vermicompost using an earthworm, Eudrilus sp. Vermicomposting depends greatly on the microorganisms, and studies on microbial diversity of vermicomposts using molecular methods have been reported. However, no information on the microbial community dynamics during the different vermicomposting stages using pyrosequencing is available. Objective: To study the bacterial community dynamics during coconut leaf...
The effects of agricultural land management practices on prokaryotic diversity are not well descr... more The effects of agricultural land management practices on prokaryotic diversity are not well described. We investigated seven management systems at the J. Phil Campbell, Sr., Natural Resource Conservation Center near Watkinsville, Georgia. Community DNA was ...
Biological diversity in soils has been linked to many functional processes. A conjoint measuremen... more Biological diversity in soils has been linked to many functional processes. A conjoint measurement of biodiversity of all three Domains (Archaea, Bacteria and Eukarya) has seldom been attempted in soils. We measured biodiversity of bacteria and eukarya (fungi, micro-and mesofauna) under controlled laboratory conditions, studying the dynamics of a detrital food web in a self-mulching Vertisol from New South Wales, Australia. Previous site use history (including vetch in the rotation) had a greater impact on biotic diversity than short-term additions of stubble.
ABSTRACT Stemming from its ability to provide order and predictability in very complex ecosystems... more ABSTRACT Stemming from its ability to provide order and predictability in very complex ecosystems, succession has survived nearly a century as a paradigm in ecosystem ecology. Soils and their microorganisms have long been considered key to ecosystem function, but the changing composition of microbial communities have not been adequately studied in the context of ecosystem development. To gain a better understanding of how bacterial communities change during soil ecosystem development, we studied their composition and diversity in soils that developed over ~77,000 years of intermittent eolian deposition.16S rRNA gene clone libraries were used to assess the diversity and composition of the communities. The bacterial community composition changed with soil age, and the overall diversity, richness and evenness of the communities increased as the soil habitat matured. Bray-Curtis ordination suggested and orderly pattern of change of the bacterial community associated with the depositional age of the soil. While the bacterial communities along the chronosequence were relatively rich, the plant diversity was low and changed in a pattern that appeared to be unrelated to changes in the bacterial communities. Microbial community change along the chronosequence, nevertheless, was reminiscent of successional processes often evoked to describe plant community change during the development of in terrestrial ecosystems.
We determined the gyrB gene sequences of all 17 hybridizations groups of Aeromonas. Phylogenetic ... more We determined the gyrB gene sequences of all 17 hybridizations groups of Aeromonas. Phylogenetic trees showing the evolutionary relatedness of gyrB and 16S rRNA genes in the type strains of Aeromonas were compared. Using this approach, we determined the phylogenetic position of Aeromonas culicicola MTCC 3249(T), isolated from midgut of Culex quinquefasciatus. In the gyrB based-analysis A. culicicola MTCC 3249(T) grouped with A. veronii whereas, it grouped with A. jandaei in the 16S rRNA based tree. The number of nucleotide differences in 16S rRNA sequences was less than found with the gyrB sequence data. Most of the observed nucleotide differences in the gyrB gene were synonymous. The Cophenetic Correlation Coefficient (CCC) for gyrB sequences was 0.87 indicating this gene to be a better molecular chronometer compared to 16S rRNA for delineation of Aeromonas species. This strain was found to be positive for the cytolytic enterotoxin gene. PCR-Amplicon Sequence Analysis (PCR-ASA) of this gene showed that the isolate is affiliated to type I and is potentially pathogenic. These PCR-ASA results agreed in part with the gyrB sequence results.
The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of... more The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of the similarities of the 16S rRNA oligonucleotide catalogs. Since then, many 16S rRNA gene sequences of newly isolated strains or clones representing the genus Methanobrevibacter have been deposited. We tried to reorganize the 16S rRNA gene sequences of this genus and revise the taxonomic affiliation of the isolates and clones representing the genus Methanobrevibacter. The phylogenetic analysis of the genus based on 786 bp aligned region from fifty-four representative sequences of the 120 available sequences for the genus revealed seven multi-member groups namely, Ruminantium, Smithii, Woesei, Curvatus, Arboriphilicus, Filiformis, and the Termite gut symbionts along with three separate lineages represented by Mbr. wolinii, Mbr. acididurans, and termite gut flagellate symbiont LHD12. The cophenetic correlation coefficient, a test for the ultrametric properties of the 16S rRNA gene sequenc...
Quorum Sensing vs Quorum Quenching: A Battle with No End in Sight, 2014
ABSTRACT Adaptation to various ecosystems is important to all microbes for growth and survival. P... more ABSTRACT Adaptation to various ecosystems is important to all microbes for growth and survival. Pathogenic microbes, especially bacteria, have developed mechanisms of synchronised expression of virulence genes with increasing population density through quorum sensing, enabling their survival in various host organisms. Due to its direct significance to humans, quorum sensing has been studied in great detail in pathogens and has significantly contributed to our understanding of microbe-host interactions. During the course of evolution, fungi have developed ways to control competing bacterial populations that co-existed. One way they achieved this is by hampering the quorum-sensing signalling amongst bacteria. Several fungal quorum sensors, metabolites, mycotoxins and enzymes secreted or produced by fungi for their communication or in response to environment are known to act as quorum-sensing inhibitors (QSIs). Farnesol, farnesoic acid isolated from Candida albicans have shown inter-species and inter-kingdom inhibition to quorum-sensing signalling. Metabolites, such as patulin and penicillic acid have shown QSI activity against bacteria. Enzymes from Aspergillus niger, Trichoderma viride and Penicillium species, such as cellulases, proteases and amylases can be used to degrade bacterial biofilms. QSIs typically utilise three different strategies: (1) inhibiting the production of quorum-sensing molecules; (2) degrading the signalling molecules; and/or (3) blocking the receptors for signalling molecules. Fungal QSIs have been successfully tested under laboratory conditions to inhibit bacteria from forming biofilms on medical equipment and reduce spoilage of processed food products. They are also a promising agent to counter increasing antibiotic-resistance amongst bacteria. Apart from agriculture and waste water treatment, fungal QSIs have potential importance for pharmaceutical and food industries as antibiotic supplement and food preservatives, respectively. This chapter discusses these aspects in fungi with a view to emphasise the need for discovering and developing novel quorum-sensing inhibitors and their potential application in industries.
We determined the gyrB gene sequences of all 17 hybridizations groups of Aeromonas. Phylogenetic ... more We determined the gyrB gene sequences of all 17 hybridizations groups of Aeromonas. Phylogenetic trees showing the evolutionary relatedness of gyrB and 16S rRNA genes in the type strains of Aeromonas were compared. Using this approach, we determined the phylogenetic position of Aeromonas culicicola MTCC 3249(T), isolated from midgut of Culex quinquefasciatus. In the gyrB based-analysis A. culicicola MTCC 3249(T) grouped with A. veronii whereas, it grouped with A. jandaei in the 16S rRNA based tree. The number of nucleotide differences in 16S rRNA sequences was less than found with the gyrB sequence data. Most of the observed nucleotide differences in the gyrB gene were synonymous. The Cophenetic Correlation Coefficient (CCC) for gyrB sequences was 0.87 indicating this gene to be a better molecular chronometer compared to 16S rRNA for delineation of Aeromonas species. This strain was found to be positive for the cytolytic enterotoxin gene. PCR-Amplicon Sequence Analysis (PCR-ASA) of this gene showed that the isolate is affiliated to type I and is potentially pathogenic. These PCR-ASA results agreed in part with the gyrB sequence results.
Soil microbial communities under three agricultural management systems (conventionally tilled cro... more Soil microbial communities under three agricultural management systems (conventionally tilled cropland, hayed pasture, and grazed pasture) and two fertilizer systems (inorganic fertilizer and poultry litter) were compared to that of a w150-y-old forest near Watkinsville, Georgia. Both 16S rRNA gene clone libraries and phospholipid fatty acid (PLFA) analyses indicated that the structure and composition of bacterial communities in the forest soil were significantly different than in the agricultural soils. Within the agricultural soils, the effect of fertilizer amendment on bacterial communities was more dramatic than either land use or season. Fertilizer amendment altered the abundance of more bacterial groups throughout the agricultural soils. In addition, the changes in the composition of bacterial groups were more pronounced in cropland than in pastures. There was much less seasonal variation between the soil libraries. Community-level differences were associated with differences in soil pH, mineralizable carbon and nitrogen, and extractable nutrients. Bacterial community diversity exhibited a complex relationship with the land use intensity in these agro-ecosystems. The pastures had the highest bacterial diversity and could be characterized as having an intermediate degree of intervention compared to low intervention in forest and high intervention in cropland. Changes in bacterial diversity could be attributed to the abundance of a few operational taxonomic units (OTUs). The microdiversity of abundant OTUs in both forest and cropland was consistent with an increase in abundance of many phenotypically similar species rather than a single species for each OTU. Soil microbial communities were significantly altered by long-term agricultural management systems, especially fertilizer amendment, and these results provide a basis for promoting conservation agricultural systems.
The response of soil microbial communities following changes in land-use is governed by multiple ... more The response of soil microbial communities following changes in land-use is governed by multiple factors. The objectives of this study were to investigate (i) whether soil microbial communities track the changes in aboveground vegetation during succession; and (ii) whether microbial communities return to their native state over time. Two successional gradients with different vegetation were studied at the W. K. Kellogg Biological Station, Michigan. The first gradient comprised a conventionally tilled cropland (CT), mid-succession forest (SF) abandoned from cultivation prior to 1951, and native deciduous forest (DF). The second gradient comprised the CT cropland, early-succession grassland (ES) restored in 1989, and long-term mowed grassland (MG). With succession, the total microbial PLFAs and soil microbial biomass C consistently increased in both gradients. While bacterial rRNA gene diversity remained unchanged, the abundance and composition of many bacterial phyla changed significantly. Moreover, microbial communities in the relatively pristine DF and MG soils were very similar despite major differences in soil properties and vegetation. After >50 years of succession, and despite different vegetation, microbial communities in SF were more similar to those in mature DF than in CT. In contrast, even after 17 years of succession, microbial communities in ES were more similar to CT than endpoint MG despite very different vegetation between CT and ES. This result suggested a lasting impact of cultivation history on the soil microbial community. With conversion of deciduous to conifer forest (CF), there was a significant change in multiple soil properties that correlated with changes in microbial biomass, rRNA gene diversity and community composition. In conclusion, history of land-use was a stronger determinant of the composition of microbial communities than vegetation and soil properties. Further, microbial communities in disturbed soils apparently return to their native state with time.
The physicochemical and biological gradients of soil and vegetative succession along the Franz Jo... more The physicochemical and biological gradients of soil and vegetative succession along the Franz Josef chronosequence in New Zealand were used to test whether bacterial communities show patterns of change associated with long-term ecosystem development. Pyrosequencing was conducted on soil-derived 16S rRNA genes at nine stages of ecosystem progression and retrogression, ranging in age from 60 to c. 120 000 years since glacial retreat. Bray-Curtis ordination indicated that the bacterial communities showed clear patterns of change that were closely aligned with ecosystem development, pedogenesis and vegetative succession (Mantel test; r = 0.58; P < 0.001). Eighty per cent (80%) of the explained variability in bacterial community structure was observed during the first c. 1000 years of development, when bacterial richness (Simpson's 1/D) declined from 130 to 30. The relatively high turnover of soil bacterial communities corresponded with an integrative 'plant-microbial successional feedback' model that predicts primarily negative feedbacks between plants and soil bacterial communities during progression and early pedogenesis. Positive feedbacks, similar to those of the plant community, could explain the long periods of community stability during later retrogressive stages of ecosystem development. This hypothesized model provides a consistent description linking belowground communities to ecosystem development and succession. The research, using deep sequencing technology, provides the first evidence for soil bacterial community change associated with the process of long-term ecosystem development. How these bacterial community changes are linked to the processes of primary ecosystem succession is not known and needs further investigation.
Soil microbial communities were examined in a chronosequence of four different land-use treatment... more Soil microbial communities were examined in a chronosequence of four different land-use treatments at the Konza Prairie Biological Station, Kansas. The time series comprised a conventionally tilled cropland (CTC) developed on former prairie soils, two restored grasslands that were initiated on former agricultural soils in 1998 (RG 98 ) and 1978 (RG 78 ), and an annually burned native tallgrass prairie (BNP), all on similar soil types. In addition, an unburned native tallgrass prairie (UNP) and another grassland restored in 2000 (RG 00 ) on a different soil type were studied to examine the effect of long-term fire exclusion vs. annual burning in native prairie and the influence of soil type on soil microbial communities in restored grasslands. Both 16S rRNA gene clone libraries and phospholipid fatty acid analyses indicated that the structure and composition of bacterial communities in the CTC soil were significantly different from those in prairie soils. Within the time series, soil physicochemical characteristics changed monotonically. However, changes in the microbial communities were not monotonic, and a transitional bacterial community formed during restoration that differed from communities in either the highly disturbed cropland or the undisturbed original prairie. The microbial communities of RG 98 and RG 00 grasslands were also significantly different even though they were restored at approximately the same time and were managed similarly; a result attributable to the differences in soil type and associated soil chemistry such as pH and Ca. Burning and seasonal effects on soil microbial communities were small. Similarly, changing plot size from 300 m 2 to 150 m 2 in area caused small differences in the estimates of microbial community structure. In conclusion, microbial community structure and biochemical properties of soil from the tallgrass prairie were strongly impacted by cultivation, and the microbial community was not fully restored even after 30 years.
The 16S-23S intergenic spacer and 23S rRNA gene sequence were determined for A. culicicola MTCC 3... more The 16S-23S intergenic spacer and 23S rRNA gene sequence were determined for A. culicicola MTCC 3249T. Ten different ISR, indicative of ten rrn operons, were found in the strain that were grouped in three major types. Of the three types, ISR I was non-coding ...
Soil is one of the largest reservoirs of prokaryotes in the biosphere, and may contain approximat... more Soil is one of the largest reservoirs of prokaryotes in the biosphere, and may contain approximately 2.6 x 10 29 cells worldwide or 5% of all the prokaryotic cells on earth. The prokaryotic diversity in soil is also enormous, with some theoretical estimates suggesting ...
In this study a microbial community suitable for anaerobic digestion of carrot pomace was develop... more In this study a microbial community suitable for anaerobic digestion of carrot pomace was developed from inocula obtained from natural environmental sources. The changes along the process were monitored using pyrosequencing of the 16S rRNA gene. As the community adapted from a diverse natural community to a community with a definite function, diversity decreased drastically. Major bacterial groups remaining after enrichment were Bacilli (31-45.3%), Porphyromonadaceae (12.1-24.8%) and Spirochaetes (12.5-18.5%). The archaeal population was even less diverse and mainly represented by a single OTU that was 99.7% similar to Methanosarcina mazei. One enrichment which failed to produce large amounts of methane had shifts in the bacterial populations and loss of methanogenic archaea.
The American journal of tropical medicine and hygiene, 2004
To describe the midgut microbial diversity and the candidate bacteria for the genetic manipulatio... more To describe the midgut microbial diversity and the candidate bacteria for the genetic manipulation for the generation of transgenic mosquitoes refractory to transmission of diseases, the microbiota of wild Culex quinquefasciatus mosquito midgut was studied using a conventional culture technique and analysis of a 16S ribosomal RNA (rRNA) gene sequence library. The culturable microbiota was identified as Acinetobacter junii, Ac. calcoaceticus, Aeromonas culicicola, Bacillus thuringiensis, Microbacterium oxydans, Pantoea agglomerans, Pseudomonas aeruginosa, Staphylococcus epidermidis, Stenotrophomonas maltophila and an unidentified bacterium from the host Drosophila paulistorium. The 16S rRNA gene library was composed of 46% unidentified and uncultured bacteria, 41% Acinetobacter spp., and 13% Lactococcus spp. The coverage calculated for the 150 clones was 83.3%. Thus, the probability of the next cloned sequence falling in a novel operational taxonomic unit (not yet observed) was 16.7%...
Study of bacterial community dynamics during coconut leaf vermicompost production and in earthwor... more Study of bacterial community dynamics during coconut leaf vermicompost production and in earthworm gut contents using pyrosequencing M. Gopal1,2, K. Jangid2, A. Gupta1,2, W.B. Whitman2, S.R. Prabhu3, G.V. Thomas1 1Microbiology Section, Central Plantation Crops Research Institute, Kasaragod, India, 2Department of Microbiology, University of Georgia, Athens, GA, USA, 3International Bio Recovery Corporation, North Vancouver, BC, Canada Background: Coconut palm (Cocos nucifera L) leaf litter, a recalcitrant waste available in large quantities in India, has been successfully recycled to vermicompost using an earthworm, Eudrilus sp. Vermicomposting depends greatly on the microorganisms, and studies on microbial diversity of vermicomposts using molecular methods have been reported. However, no information on the microbial community dynamics during the different vermicomposting stages using pyrosequencing is available. Objective: To study the bacterial community dynamics during coconut leaf...
The effects of agricultural land management practices on prokaryotic diversity are not well descr... more The effects of agricultural land management practices on prokaryotic diversity are not well described. We investigated seven management systems at the J. Phil Campbell, Sr., Natural Resource Conservation Center near Watkinsville, Georgia. Community DNA was ...
Biological diversity in soils has been linked to many functional processes. A conjoint measuremen... more Biological diversity in soils has been linked to many functional processes. A conjoint measurement of biodiversity of all three Domains (Archaea, Bacteria and Eukarya) has seldom been attempted in soils. We measured biodiversity of bacteria and eukarya (fungi, micro-and mesofauna) under controlled laboratory conditions, studying the dynamics of a detrital food web in a self-mulching Vertisol from New South Wales, Australia. Previous site use history (including vetch in the rotation) had a greater impact on biotic diversity than short-term additions of stubble.
ABSTRACT Stemming from its ability to provide order and predictability in very complex ecosystems... more ABSTRACT Stemming from its ability to provide order and predictability in very complex ecosystems, succession has survived nearly a century as a paradigm in ecosystem ecology. Soils and their microorganisms have long been considered key to ecosystem function, but the changing composition of microbial communities have not been adequately studied in the context of ecosystem development. To gain a better understanding of how bacterial communities change during soil ecosystem development, we studied their composition and diversity in soils that developed over ~77,000 years of intermittent eolian deposition.16S rRNA gene clone libraries were used to assess the diversity and composition of the communities. The bacterial community composition changed with soil age, and the overall diversity, richness and evenness of the communities increased as the soil habitat matured. Bray-Curtis ordination suggested and orderly pattern of change of the bacterial community associated with the depositional age of the soil. While the bacterial communities along the chronosequence were relatively rich, the plant diversity was low and changed in a pattern that appeared to be unrelated to changes in the bacterial communities. Microbial community change along the chronosequence, nevertheless, was reminiscent of successional processes often evoked to describe plant community change during the development of in terrestrial ecosystems.
We determined the gyrB gene sequences of all 17 hybridizations groups of Aeromonas. Phylogenetic ... more We determined the gyrB gene sequences of all 17 hybridizations groups of Aeromonas. Phylogenetic trees showing the evolutionary relatedness of gyrB and 16S rRNA genes in the type strains of Aeromonas were compared. Using this approach, we determined the phylogenetic position of Aeromonas culicicola MTCC 3249(T), isolated from midgut of Culex quinquefasciatus. In the gyrB based-analysis A. culicicola MTCC 3249(T) grouped with A. veronii whereas, it grouped with A. jandaei in the 16S rRNA based tree. The number of nucleotide differences in 16S rRNA sequences was less than found with the gyrB sequence data. Most of the observed nucleotide differences in the gyrB gene were synonymous. The Cophenetic Correlation Coefficient (CCC) for gyrB sequences was 0.87 indicating this gene to be a better molecular chronometer compared to 16S rRNA for delineation of Aeromonas species. This strain was found to be positive for the cytolytic enterotoxin gene. PCR-Amplicon Sequence Analysis (PCR-ASA) of this gene showed that the isolate is affiliated to type I and is potentially pathogenic. These PCR-ASA results agreed in part with the gyrB sequence results.
The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of... more The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of the similarities of the 16S rRNA oligonucleotide catalogs. Since then, many 16S rRNA gene sequences of newly isolated strains or clones representing the genus Methanobrevibacter have been deposited. We tried to reorganize the 16S rRNA gene sequences of this genus and revise the taxonomic affiliation of the isolates and clones representing the genus Methanobrevibacter. The phylogenetic analysis of the genus based on 786 bp aligned region from fifty-four representative sequences of the 120 available sequences for the genus revealed seven multi-member groups namely, Ruminantium, Smithii, Woesei, Curvatus, Arboriphilicus, Filiformis, and the Termite gut symbionts along with three separate lineages represented by Mbr. wolinii, Mbr. acididurans, and termite gut flagellate symbiont LHD12. The cophenetic correlation coefficient, a test for the ultrametric properties of the 16S rRNA gene sequenc...
Quorum Sensing vs Quorum Quenching: A Battle with No End in Sight, 2014
ABSTRACT Adaptation to various ecosystems is important to all microbes for growth and survival. P... more ABSTRACT Adaptation to various ecosystems is important to all microbes for growth and survival. Pathogenic microbes, especially bacteria, have developed mechanisms of synchronised expression of virulence genes with increasing population density through quorum sensing, enabling their survival in various host organisms. Due to its direct significance to humans, quorum sensing has been studied in great detail in pathogens and has significantly contributed to our understanding of microbe-host interactions. During the course of evolution, fungi have developed ways to control competing bacterial populations that co-existed. One way they achieved this is by hampering the quorum-sensing signalling amongst bacteria. Several fungal quorum sensors, metabolites, mycotoxins and enzymes secreted or produced by fungi for their communication or in response to environment are known to act as quorum-sensing inhibitors (QSIs). Farnesol, farnesoic acid isolated from Candida albicans have shown inter-species and inter-kingdom inhibition to quorum-sensing signalling. Metabolites, such as patulin and penicillic acid have shown QSI activity against bacteria. Enzymes from Aspergillus niger, Trichoderma viride and Penicillium species, such as cellulases, proteases and amylases can be used to degrade bacterial biofilms. QSIs typically utilise three different strategies: (1) inhibiting the production of quorum-sensing molecules; (2) degrading the signalling molecules; and/or (3) blocking the receptors for signalling molecules. Fungal QSIs have been successfully tested under laboratory conditions to inhibit bacteria from forming biofilms on medical equipment and reduce spoilage of processed food products. They are also a promising agent to counter increasing antibiotic-resistance amongst bacteria. Apart from agriculture and waste water treatment, fungal QSIs have potential importance for pharmaceutical and food industries as antibiotic supplement and food preservatives, respectively. This chapter discusses these aspects in fungi with a view to emphasise the need for discovering and developing novel quorum-sensing inhibitors and their potential application in industries.
We determined the gyrB gene sequences of all 17 hybridizations groups of Aeromonas. Phylogenetic ... more We determined the gyrB gene sequences of all 17 hybridizations groups of Aeromonas. Phylogenetic trees showing the evolutionary relatedness of gyrB and 16S rRNA genes in the type strains of Aeromonas were compared. Using this approach, we determined the phylogenetic position of Aeromonas culicicola MTCC 3249(T), isolated from midgut of Culex quinquefasciatus. In the gyrB based-analysis A. culicicola MTCC 3249(T) grouped with A. veronii whereas, it grouped with A. jandaei in the 16S rRNA based tree. The number of nucleotide differences in 16S rRNA sequences was less than found with the gyrB sequence data. Most of the observed nucleotide differences in the gyrB gene were synonymous. The Cophenetic Correlation Coefficient (CCC) for gyrB sequences was 0.87 indicating this gene to be a better molecular chronometer compared to 16S rRNA for delineation of Aeromonas species. This strain was found to be positive for the cytolytic enterotoxin gene. PCR-Amplicon Sequence Analysis (PCR-ASA) of this gene showed that the isolate is affiliated to type I and is potentially pathogenic. These PCR-ASA results agreed in part with the gyrB sequence results.
Soil microbial communities under three agricultural management systems (conventionally tilled cro... more Soil microbial communities under three agricultural management systems (conventionally tilled cropland, hayed pasture, and grazed pasture) and two fertilizer systems (inorganic fertilizer and poultry litter) were compared to that of a w150-y-old forest near Watkinsville, Georgia. Both 16S rRNA gene clone libraries and phospholipid fatty acid (PLFA) analyses indicated that the structure and composition of bacterial communities in the forest soil were significantly different than in the agricultural soils. Within the agricultural soils, the effect of fertilizer amendment on bacterial communities was more dramatic than either land use or season. Fertilizer amendment altered the abundance of more bacterial groups throughout the agricultural soils. In addition, the changes in the composition of bacterial groups were more pronounced in cropland than in pastures. There was much less seasonal variation between the soil libraries. Community-level differences were associated with differences in soil pH, mineralizable carbon and nitrogen, and extractable nutrients. Bacterial community diversity exhibited a complex relationship with the land use intensity in these agro-ecosystems. The pastures had the highest bacterial diversity and could be characterized as having an intermediate degree of intervention compared to low intervention in forest and high intervention in cropland. Changes in bacterial diversity could be attributed to the abundance of a few operational taxonomic units (OTUs). The microdiversity of abundant OTUs in both forest and cropland was consistent with an increase in abundance of many phenotypically similar species rather than a single species for each OTU. Soil microbial communities were significantly altered by long-term agricultural management systems, especially fertilizer amendment, and these results provide a basis for promoting conservation agricultural systems.
The response of soil microbial communities following changes in land-use is governed by multiple ... more The response of soil microbial communities following changes in land-use is governed by multiple factors. The objectives of this study were to investigate (i) whether soil microbial communities track the changes in aboveground vegetation during succession; and (ii) whether microbial communities return to their native state over time. Two successional gradients with different vegetation were studied at the W. K. Kellogg Biological Station, Michigan. The first gradient comprised a conventionally tilled cropland (CT), mid-succession forest (SF) abandoned from cultivation prior to 1951, and native deciduous forest (DF). The second gradient comprised the CT cropland, early-succession grassland (ES) restored in 1989, and long-term mowed grassland (MG). With succession, the total microbial PLFAs and soil microbial biomass C consistently increased in both gradients. While bacterial rRNA gene diversity remained unchanged, the abundance and composition of many bacterial phyla changed significantly. Moreover, microbial communities in the relatively pristine DF and MG soils were very similar despite major differences in soil properties and vegetation. After >50 years of succession, and despite different vegetation, microbial communities in SF were more similar to those in mature DF than in CT. In contrast, even after 17 years of succession, microbial communities in ES were more similar to CT than endpoint MG despite very different vegetation between CT and ES. This result suggested a lasting impact of cultivation history on the soil microbial community. With conversion of deciduous to conifer forest (CF), there was a significant change in multiple soil properties that correlated with changes in microbial biomass, rRNA gene diversity and community composition. In conclusion, history of land-use was a stronger determinant of the composition of microbial communities than vegetation and soil properties. Further, microbial communities in disturbed soils apparently return to their native state with time.
The physicochemical and biological gradients of soil and vegetative succession along the Franz Jo... more The physicochemical and biological gradients of soil and vegetative succession along the Franz Josef chronosequence in New Zealand were used to test whether bacterial communities show patterns of change associated with long-term ecosystem development. Pyrosequencing was conducted on soil-derived 16S rRNA genes at nine stages of ecosystem progression and retrogression, ranging in age from 60 to c. 120 000 years since glacial retreat. Bray-Curtis ordination indicated that the bacterial communities showed clear patterns of change that were closely aligned with ecosystem development, pedogenesis and vegetative succession (Mantel test; r = 0.58; P < 0.001). Eighty per cent (80%) of the explained variability in bacterial community structure was observed during the first c. 1000 years of development, when bacterial richness (Simpson's 1/D) declined from 130 to 30. The relatively high turnover of soil bacterial communities corresponded with an integrative 'plant-microbial successional feedback' model that predicts primarily negative feedbacks between plants and soil bacterial communities during progression and early pedogenesis. Positive feedbacks, similar to those of the plant community, could explain the long periods of community stability during later retrogressive stages of ecosystem development. This hypothesized model provides a consistent description linking belowground communities to ecosystem development and succession. The research, using deep sequencing technology, provides the first evidence for soil bacterial community change associated with the process of long-term ecosystem development. How these bacterial community changes are linked to the processes of primary ecosystem succession is not known and needs further investigation.
Soil microbial communities were examined in a chronosequence of four different land-use treatment... more Soil microbial communities were examined in a chronosequence of four different land-use treatments at the Konza Prairie Biological Station, Kansas. The time series comprised a conventionally tilled cropland (CTC) developed on former prairie soils, two restored grasslands that were initiated on former agricultural soils in 1998 (RG 98 ) and 1978 (RG 78 ), and an annually burned native tallgrass prairie (BNP), all on similar soil types. In addition, an unburned native tallgrass prairie (UNP) and another grassland restored in 2000 (RG 00 ) on a different soil type were studied to examine the effect of long-term fire exclusion vs. annual burning in native prairie and the influence of soil type on soil microbial communities in restored grasslands. Both 16S rRNA gene clone libraries and phospholipid fatty acid analyses indicated that the structure and composition of bacterial communities in the CTC soil were significantly different from those in prairie soils. Within the time series, soil physicochemical characteristics changed monotonically. However, changes in the microbial communities were not monotonic, and a transitional bacterial community formed during restoration that differed from communities in either the highly disturbed cropland or the undisturbed original prairie. The microbial communities of RG 98 and RG 00 grasslands were also significantly different even though they were restored at approximately the same time and were managed similarly; a result attributable to the differences in soil type and associated soil chemistry such as pH and Ca. Burning and seasonal effects on soil microbial communities were small. Similarly, changing plot size from 300 m 2 to 150 m 2 in area caused small differences in the estimates of microbial community structure. In conclusion, microbial community structure and biochemical properties of soil from the tallgrass prairie were strongly impacted by cultivation, and the microbial community was not fully restored even after 30 years.
The 16S-23S intergenic spacer and 23S rRNA gene sequence were determined for A. culicicola MTCC 3... more The 16S-23S intergenic spacer and 23S rRNA gene sequence were determined for A. culicicola MTCC 3249T. Ten different ISR, indicative of ten rrn operons, were found in the strain that were grouped in three major types. Of the three types, ISR I was non-coding ...
Soil is one of the largest reservoirs of prokaryotes in the biosphere, and may contain approximat... more Soil is one of the largest reservoirs of prokaryotes in the biosphere, and may contain approximately 2.6 x 10 29 cells worldwide or 5% of all the prokaryotic cells on earth. The prokaryotic diversity in soil is also enormous, with some theoretical estimates suggesting ...
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Papers by Kamlesh Jangid