Microbial Functional Gene Diversity Research Articles

Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic

Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.

Niche-dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis.

Most researches on sponge holobionts focus primarily on symbiotic microbes, yet data at the level of the sponge hologenome are still relatively scarce. Understanding of the sponge host and its microbial gene expression profiles and the host-microbes interplay in different niches represents a key aspect of sponge hologenome. Using the Hawaiian demosponge Mycale grandis in different niches as a model, i.e. on rocks, on the surface of coral Porites compressa, under alga Gracilaria salicornia, we compared the bacterial and fungal community structure, functional gene diversity, expression pattern and the host transcriptome by integrating open-format (deep sequencing) and closed-format (GeoChip microarray) high-throughput techniques. Little inter-niche variation in bacterial and fungal phylogenetic diversity was detected for M. grandis in different niches, but a clear niche-dependent variability in the functional gene diversity and expression pattern of M. grandis host and its symbiotic microbiota was uncovered by GeoChip microarray and transcriptome analyses. Particularly, sponge host genes related to innate immunity and microbial recognition showed a strong correlation with the microbial symbionts' functional gene diversity and transcriptional richness in different niches. The cross-niche variability with respect to the symbiont functional gene diversity and the transcriptional richness of M. grandis holobiont putatively reflects the interplay of niche-specific selective pressure and the symbiont functional diversity. Niche-dependent gene expression profiles of M. grandis hologenome and the host-microbes interplay were suggested though little inter-niche variation in bacterial and fungal diversity was detected, particularly the sponge innate immunity was found to be closely related to the symbiotic microbes. Altogether, these findings provide novel insights into the black box of one sponge holobiont in different niches at the hologenome level.

Metagenomics and metabolomics reveal that gut microbiome adapts to the diet transition in Hyla rabbits

There is still a lack of longitudinal dynamic studies on the taxonomic features, functional reserves, and metabolites of the rabbit gut microbiome. An experiment was conducted to characterize the bacterial community of rabbits. By combining metagenomics and metabolomics, we have comprehensively analyzed the longitudinal dynamics of the rabbit gut microbiota and its effect on host adaptability. Our data reveal an overall increasing trend in microbial community and functional gene diversity and richness during the pre-harvest lifespan of rabbits. The introduction of solid feed is an important driving factor affecting rabbit gut microbiological compositions. Clostridium and Ruminococcus had significantly higher relative abundances in the solid feed stage. Further, the starch and fiber in solid feed promote the secretion of carbohydrate-degrading enzymes, which helps the host adapt to dietary changes. The rabbit gut microbiota can synthesize lysine, and the synthase is gradually enriched during the diet transformation. The gut microbiota of newborn rabbits has a higher abundance of lipid metabolism, which helps the host obtain more energy from breast milk lipids. The rabbit gut microbiota can also synthesize a variety of secondary bile acids after the introduction of solid feed. These findings provide a novel understanding of how the gut microbiota mediates adaptability to environment and diet in rabbits and provide multiple potential strategies for regulating intestinal health and promoting higher feed efficiency.

Biogeography and diversity patterns of functional genes associated with C, N, P, S cycling processes across China classical sea sediments

Microbial activities influence the ecological functions of marine ecosystems and play an essential role in biogeochemical cycling. However, there are more studies on microbial diversity and community structure, and few reports have explored nutrient cycling processes by microbial functional gene abundance and diversity. Given these limitations, in order to investigate the variability of nutrient cycling among different sea areas and its influencing factors, the sediments of the Bohai Sea, Yellow Sea, East China Sea and South China Sea were used in this study. The number of average copies of each functional gene was obtained by the quantitative microbial element cycling (QMEC) smart chip. A total of 65 functional genes related to C, N, P and S cycling were identified, and the results showed that all functional genes decreased in the order of magnitude from the Bohai Sea to the East China Sea, Yellow Sea and South China Sea, and the abundance of functional genes was significantly higher at the sampling sites near the land side, which related to human activities. Additionally, NH4+, organic carbon, total carbon and geographical factor were the main driving factors of functional gene composition changes (p < 0.05), and all functional genes were significantly correlated with total carbon and geographical distance (p < 0.01). These findings further expand the understanding of marine ecosystems and provide robust support for global biogeochemical cycles.

Humic Lake Exhibits Higher Microbial Functional Gene Diversity and Weaker Gene Interaction Efficiency than a Common Alkaline Lake.

Simple SummaryThe humic lake represents a special kind of aquatic ecosystem with high humic substances, low irradiance, and a high potential for greenhouse gas emissions. Despite the special environment and biogeochemical processes in humic lake water, knowledge about the underlying microbial-driven functions remains elusive. Here, we studied the compositions and functional gene structures of microbial communities in a humic lake (HL) and a reference weakly alkaline lake (RAL). We found that the high organic matter content in the HL supported higher gene diversity; and, specifically, the carbon and nitrogen fixations, the degradation of various types of carbon, methane oxidation and methanogenesis, ammonification, denitrification, and assimilatory N reduction might be enhanced more in the HL than in the RAL. By contrast, the humic fractions in the HL might reduce microbial metabolic potential for sulfur oxidation and phosphorus degradation. The potential interactions between different functional microorganisms might be down-regulated provided that there were more easily acquired nutrients in the HL. Overall, our results showed the functional gene “landscape” of microbial communities in the surface water of a humic lake, which helps understand the biogeochemical processes and the remediation of organic matter pollution in lacustrine ecosystems.Humic lakes (HLs) are special water bodies (high organic matter content, low pH, and low transparency) that are important sources of major greenhouse gases. The knowledge about microbial functional potentials and the interactions among different genes in HL water has been scarcely understood. In this study, we used 16S rRNA gene sequencing and the GeoChip 5.0 to investigate microbial community compositions and functional gene structures in an HL and a reference weakly alkaline lake (RAL). The HL microbial communities showed distinct compositions and functional gene structures than those in the RAL. The functional gene diversity was significantly higher in the HL than in the RAL. Specifically, higher gene relative intensities in carbon and nitrogen fixations, the degradation of various types of carbon, methane oxidation and methanogenesis, ammonification, denitrification, and assimilatory N reduction were observed in the HL samples. By contrast, the metabolic potentials of microorganisms involved in dissimilatory N reduction, phosphorus degradation, and sulfur oxidation were weaker in the HL than in the RAL. Despite higher functional gene diversity, the interaction efficiency among genes (reflected by network geodesic distance and clustering coefficient) might be reduced in the HL. Different functional microbes may develop less interdependent relationships in acquiring nutrients given the high resource availability in the HL. Overall, the enhanced microbial metabolic potentials and less efficient functional interactions might have great consequences on nutrient cycling and greenhouse gas emissions in the HL ecosystem.

Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories.

Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO3) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.

Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere.

Soil fertility is a function of the level of organic and inorganic substances present in the soil, and it influences the activities of soil-borne microbes, plant growth performance and a host of other beneficial ecological functions. In this metagenomics study, we evaluated the response of maize microbial functional gene diversity involved in chemotaxis, antibiotics, siderophores, and antifungals producing genes within the rhizosphere of maize plants under compost, inorganic fertilizer, and unfertilized conditions. The results show that fertilization treatments at higher compost manure and lower inorganic fertilizer doses as well as maize plants itself in the unfertilized soil through rhizosphere effects share similar influences on the abundance of chemotaxis, siderophores, antifungal, and antibiotics synthesizing genes present in the samples, while higher doses of inorganic fertilizer and lower compost manure treatments significantly repress these genes. The implication is for a disease suppressive soil to be achieved, soil fertilization with high doses of compost manure fertilizer treatments as well as lower inorganic fertilizer should be used to enrich soil fertility and boost the abundance of chemotaxis and disease suppressive genes. Maize crops also should be planted sole or intercropped with other crops to enhance the rhizosphere effect of these plants in promoting the expression and abundance of these beneficial genes in the soil.

Soil aggregate size-dependent relationships between microbial functional diversity and multifunctionality

Soil stability and aggregates are important drivers of soil fertility and microbial diversity and are highly vulnerable to land degradation. However, the role of soil aggregates in driving the responses of microbial functional diversity and multiple ecosystem services and functions (multifunctionality) to further degradation (e.g., fertilization) remains largely unexplored and poorly understood. In this study, we used soils from long-term experiments involving inorganic and organic fertilization treatments to investigate the role soil aggregates (microscale) play in driving microbial functional gene diversity (via GeoChip) and the activity of multiple extracellular enzymes in an agricultural ecosystem. We found that microbial functional gene diversity has a significant and positive relationship with soil multifunctionality, which is enhanced in soil aggregates by organic fertilizer but is reduced by inorganic fertilizer. We also found that soil aggregate fractions indirectly controlled multiple ecosystem functions via changes in functional diversity. Smaller soil aggregates with higher resource availability (carbon and nitrogen) supported more ecological functions than larger aggregates under contrasting fertilizer management regimes. Soil multifunctionality is regulated by the differences in resource availability and not by microbial functional gene composition, which suggests that microbial functional diversity contributed more to multifunctionality than gene composition. Random forest analysis and structural equation modeling indicated that soil carbon and nitrogen and microbial functional diversity together determined the multifunctionality, whereas soil traits have more standardized total effects than functional diversity. Our study highlights that soil aggregation stratifies soil nutrition and microbial functional diversity, which leads to the differentiation of aggregate ecosystem multifunctionality.

Climate mediates continental scale patterns of stream microbial functional diversity

BackgroundUnderstanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce for microorganisms, especially in freshwater ecosystems. Here we study 15,289 functional genes of stream biofilm microbes along three elevational gradients in Norway, Spain and China.ResultsWe find that alpha diversity declines towards high elevations and assemblage composition shows increasing turnover with greater elevational distances. These elevational patterns are highly consistent across mountains, kingdoms and functional categories and exhibit the strongest trends in China due to its largest environmental gradients. Across mountains, functional gene assemblages differ in alpha diversity and composition between the mountains in Europe and Asia. Climate, such as mean temperature of the warmest quarter or mean precipitation of the coldest quarter, is the best predictor of alpha diversity and assemblage composition at both mountain and continental scales, with local non-climatic predictors gaining more importance at mountain scale. Under future climate, we project substantial variations in alpha diversity and assemblage composition across the Eurasian river network, primarily occurring in northern and central regions, respectively.ConclusionsWe conclude that climate controls microbial functional gene diversity in streams at large spatial scales; therefore, the underlying ecosystem processes are highly sensitive to climate variations, especially at high latitudes. This biogeographical framework for microbial functional diversity serves as a baseline to anticipate ecosystem responses and biogeochemical feedback to ongoing climate change.BSweEpkETcG1op9mYTCivQVideo

Microbial functional gene diversity in natural secondary forest Ultisols

The diversity and biogeography of functional genes at a regional scale remains unclear. We hypothesize that plant community composition, nutrient availability, and spatial distance are driving factors for the functional gene diversity of soil microorganisms at a regional scale. We also hypothesize that different functional genes have different responses to environment. Using functional gene arrays (GeoChip 3.0), we examined microbial diversity, and influencing factors in Ultisols in 11 natural secondary forest plots in southern China which contained 4073 functional genes averagely. Carbon and nitrogen cycle genes were more variable than genes involved in phosphorus utilization, organic remediation, and metal resistance, in similar trends with soil substrate availability. Genes involved in nitrification being more variable than other nitrogen cycling genes; phytase genes being more variable than polyphosphate kinase genes (ppk) and exopolyphosphatase genes (ppx); exoglucanase and endoglucanase genes being more variable than cellobiase genes; lignin peroxidase genes (lip) being more variable than manganese peroxidase genes (mnp). Approximately 41% of the variation in gene composition could be explained by fine root surface area, available nitrogen, and the largest spatial scale factor, with the former two environmental factors over influenced spatial distance. Both environmental factors (represented by nutrient availability) and spatial distance influenced microbial functional gene composition, while the influence of spatial distance worked through environmental factors in natural secondary forest in Ultisols within approximately 500 km, providing insights into microbial biogeography from a functional gene perspective.

Application of biogas slurry rather than biochar increases soil microbial functional gene signal intensity and diversity in a poplar plantation

Microbes play critical roles in the cycling of nutrients in forest ecosystems. Many studies have shown that the application of organic fertilizer can alter bacterial diversity; however, the responses of soil microbial functional genes to organic fertilization (particularly biogas slurry fertilization, or in combination with biochar) have not been elucidated as yet. We examined the responses of the abundance, diversity, and composition of soil microbial functional genes under five-years of fertilization. This fertilization involved low and high application rates of biogas slurry, at 250 and 375 m3 ha−1 yr−1, respectively, or in combination with low and high application rates of biochar, at 80 and 120 t ha−1, respectively, in a coastal poplar plantation of Eastern China. Compared to the control, the normalized signal intensity of genes in the major functional categories increased significantly in response to the quantity of applied biogas slurry, but insignificantly in response to the additional application of biochar. Subsequent to the application of biogas slurry, the functional gene evenness and Shannon index increased significantly; however, the addition of biochar to the biogas slurry had insignificant effects on the α-diversity of functional genes. These functional gene compositions under five different treatments were well distinguished, primarily through the application of biogas slurry. Our results revealed that the abundance of a large number of key functional genes involved in C, N, and P cycling were effectively increased, and these changes were well correlated with most soil properties. This study reveals the molecular level mechanisms that promote plant growth following organic fertilizer application, through the enhancement of soil microbial functional gene diversity.

Microbial functional gene patterns related to soil greenhouse gas emissions in oil contaminated areas

Linking microbial community structure to physiology and ecological processes is a critical focus of microbial ecology. To understand the microbial functional gene patterns related to soil greenhouse gas [carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O)] emissions under oil contamination, we used functional gene array (GeoChip 5.0) analysis and network methods to investigate the feedback responses of soil microbial functional gene patterns and identify keystone genes in Shengli Oilfield, China. The microbial functional gene number, relative abundance and diversity involved in carbon degradation and nitrogen cycling decreased consistently with the reduced CO2 and N2O flux in oil contaminated soils, whereas the gene number and relative abundance of methane-production related genes increased with contamination. Functional molecular ecological networks were built based on random matrix theory, where network structures and properties showed significantly variation between oil contaminated and uncontaminated soils (P<0.05). Network nodes, connectivity and complexity all reduced under oil contamination. The sensitive and the highest connective genes in the network were identified as keystone genes, based on Mann-Whitney U tests and network analysis. Our findings improved the understanding of the microbe-mediated mechanisms affecting soil greenhouse gas emissions.

Responses of bulk and rhizosphere soil microbial communities to thermoclimatic changes in a Mediterranean ecosystem

The effect of thermoclimatic changes on microbial communities in the rhizosphere of a wild thyme species, Thymus zygis L., and its surrounding bulk soil was studied along elevational gradients in the Sierra Nevada National Park (Spain). Multiplex amplicon sequencing of bacterial and fungal taxonomic markers revealed that the richness, diversity and structure of bacterial and fungal communities were affected by thermoclimatic changes, with environmental parameters (mean annual atmospheric temperature and precipitation) and edaphic properties (mainly pH and nutrients) as the major drivers. Although both bulk soil and rhizosphere communities were structured according to the thermoclimatic zones, the response of microorganisms to thermoclimatic changes was different depending on the rhizosphere effect. On the contrary, the microbial functional gene diversity was not affected by thermoclimatic changes suggesting functional redundancy in the microbial communities along the altitudinal gradients. However, the functional gene diversity was clearly different between bulk soil and the rhizosphere, with the latter harbouring a larger number of gene copies and more different functional genes than bulk soils. Finally, a set of microbial bioindicators are defined for the thermoclimatic zones as a starting point to develop improved biological tools and models to monitor and predict the effects of climate changes. To the best of our knowledge, this is the first study where the response of bulk soil and rhizosphere microbial communities to thermoclimatic changes has been studied in parallel.

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain.

The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500–2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change.

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.

BackgroundTropical rainforests cover over 50 % of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology.ResultsGene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure.ConclusionsOverall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0491-8) contains supplementary material, which is available to authorized users.

Analyses of the influencing factors of soil microbial functional gene diversity in tropical rainforest based on GeoChip 5.0.

To examine soil microbial functional gene diversity and causative factors in tropical rainforests, we used a microarray-based metagenomic tool named GeoChip 5.0 to profile it. We found that high microbial functional gene diversity and different soil microbial metabolic potential for biogeochemical processes were considered to exist in tropical rainforest. Soil available nitrogen was the most associated with soil microbial functional gene structure. Here, we mainly describe the experiment design, the data processing, and soil biogeochemical analyses attached to the study in details, which could be published on BMC microbiology Journal in 2015, whose raw data have been deposited in NCBI's Gene Expression Omnibus (accession number GSE69171).

Redox potential and microbial functional gene diversity in wetland sediments under simulated warming conditions: implications for phosphorus mobilization

Microbial-driven biogeochemical cycles in wetlands impacted by global warming pose a potential downstream eutrophication risk. However, the consequences of ongoing warming on the functional and metabolic potential of sediment microbial communities are largely unknown. We incubated sediment samples under both ambient temperature conditions (control) and simulated warming conditions of 5°C above ambient temperature (warmed) using a novel field microcosm system. In warmed samples, we observed in situ a decreased thickness of the oxidized sediment layer and associated lower sediment redox potential. GeoChip 4.0, a comprehensive functional gene microarray, demonstrated that many functional genes that are involved in oxidation–reduction reactions and in phosphorus (P) degradation were preferentially enriched under warming conditions. The enriched genes included those genes encoding carbon monoxide dehydrogenase, acetyl-CoA carboxylase biotin carboxylase (ppc), and ribulose-1,5-bisphosphate carboxylase (Rubisco) for carbon fixation; nitrate reductases (narG) and nitrous oxide reductases (nosZ) for denitrification; cytochrome c for metal reduction; and exopolyphosphatase (ppx) for polyphosphate degradation. The redox potential was one of the most significant parameters linked to microbial functional gene structure. These results demonstrate that the enhanced hypoxia and anaerobic metabolic pathways accelerated sediment P mobilization in freshwater wetland subject to warming, raising the potential of water eutrophication.

Soil microbial gene diversity in natural broadleaf forests on Gaoligongshan Mountain

Soil microorganisms are among the most important ecosystem components, and they play key roles in biogeochemical cycling, such as carbon and nitrogen cycling. Because of limits in methodology, our understanding of the detailed biological processes in soil microbial communities and their functional activity remains limited. In this study, soil microbial functional gene diversity in broadleaf forests on Gaoligongshan Mountain, Yunnan Province, China, was analyzed by Geochip 2.0, a microbial functional gene array. The array contained 24243 oligonucleotide probes from over 150 functional gene families that targeted key functional genes involved in various ecological and environmental processes, such as carbon and nitrogen cycling. Thus, it provided rapid, specific, sensitive, and potentially quantitative data on microbial communities and was useful for studying the functional diversity and dynamics of microbial communities in different natural environments. A total of 2273 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process, and other categories were detected in five soil samples, and their Shannon-Weaver indexes ranged from 5.39 to 6.91. The soil microbial diversity and abundance in evergreen broadleaf forest was higher than in coniferous and deciduous broadleaf forests. Fifteen and twelve gene categories involved in carbon and nitrogen cycling were observed, respectively. The diversity and abundance of genes involved in carbon and nitrogen cycling differed among the sampling sites. These results showed that different microbial processes involved in element cycling existed in these soil-sampling sites. Canonical correspondence analysis showed that soil organic carbon, soil moisture, soil temperature, and plant diversity may be the key environmental variables shaping the microbial community structure. Variation partitioning analysis showed that soil moisture, soil temperature, and plant Shannon-Weaver index can explain 25.79%, 25.83%, and 18.94% of the community composition, respectively.

An Integrated Study to Analyze Soil Microbial Community Structure and Metabolic Potential in Two Forest Types

Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (P<0.05) at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05) correlation was existed between the soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (P<0.05) to the relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.

Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau

BackgroundGeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau.ResultsA total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P < 0.05) correlated with the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes.ConclusionsHigh overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were significantly impacted by local environmental conditions, and soil C/N is the most important factor to impact the microbial structure in alpine meadow in Qinghai-Tibetan plateau.