Role Of Microbial Community Composition Research Articles

Fungal traits help to understand the decomposition of simple and complex plant litter.

Litter decomposition is a key ecosystem process, relevant for the release and storage of nutrients and carbon in soil. Soil fungi are one of the dominant drivers of organic matter decomposition, but fungal taxa differ substantially in their functional ability to decompose plant litter. Knowledge is mostly based on observational data and subsequent molecular analyses and in vitro studies have been limited to forest ecosystems. In order to better understand functional traits of saprotrophic soil fungi in grassland ecosystems, we isolated 31 fungi from a natural grassland and performed several in vitro studies testing for i) leaf and wood litter decomposition, ii) the ability to use carbon sources of differing complexity, iii) the enzyme repertoire. Decomposition strongly varied among phyla and isolates, with Ascomycota decomposing the most and Mucoromycota decomposing the least. The phylogeny of the fungi and their ability to use complex carbon were the most important predictors for decomposition. Our findings show that it is crucial to understand the role of individual members and functional groups within the microbial community. This is an important way forward to understand the role of microbial community composition for the prediction of litter decomposition and subsequent potential carbon storage in grassland soils.

Community Level Physiological Profiling of Microbial Communities Influencing Mine Spoil Genesis in Chronosequence Coal Mine Overburden Spoil

Ecological restoration through mine spoil genesis should be dogmatic and the strategies involved a holistic approach, which emphasizes the role of microbial community composition that varies in accordance with the physiological and nutritional status of mine spoil profiles. This is because the patterns observed aboveground is being driven by the belowground diversity and processes. Thus, the relationship between microbial community structure and mine spoil genesis in chronosequence coal mine spoil has attracted considerable research attention. The occurrence of higher microbial diversity and difficulties in culturing microbes necessitate the use of a culture-independent approach through community-level physiological profiling based on the patterns of carbon source utilization using BIOLOG Ecoplate and thereby the functional diversity of microbial communities in different age series coal mine spoil was determined. The average well-color development exhibited an increasing trend with a minimum in OB0 (0.0640) and a maximum in OB15 (0.5060) over time. The patterns of substrate utilization (carbohydrates, carboxylic and ketonic acids, amino acids, polymers, amines, and amides) reflect the shift in microbial community composition in different age series coal mine spoil over time. Gradual increase in species richness and Shannon diversity index with the increase in age of mine spoil substantiated relatively higher microbial diversity reflecting the sign of mine spoil genesis. Principal component analysis and redundancy analysis based on the differential patterns of substrate utilization discriminate different age series coal mine spoil into independent clusters, which evaluated the broad-scale patterns of microbial community dynamics influencing the pace and progress of mine spoil genesis.

Microbial assimilation dynamics differs but total mineralization from added root and shoot residues is similar in agricultural Alfisols

Microbial transformation of crop residue is the key process of soil organic matter (SOM) formation and mineralization, which determines soil fertility and affects global climate change. However, utilization dynamics of residue-derived carbon (residue C) by various microbial communities is still not well understood, especially under different residue quality and soil fertility conditions over a long-term scale (i.e., >1 year). In this study, a 500-day in-situ field experiment was conducted using 13C-labeled maize (Zea mays L.) root and shoot (composed of both stem and leaf) to examine the role of microbial community composition on the C processing. Specifically, the mineralization of residue C and incorporation of residue C into microbial biomass in low fertility (LF) and high fertility (HF) soils were investigated. The abundance of 13C in soil samples and microbial phospholipid fatty acids (PLFAs) were measured after 60, 90, 150 and 500 days since the residues added. The results showed that the mineralization rate of residue C was significantly higher in the LF than that in the HF soil for the first 150 days, and the shoot-derived C was more susceptible to degradation than root-derived C, but the final mineralization rates (~78%) were not significantly different among treatments on the day 500. Soil fertility significantly affected the relative composition of different microbial groups and distribution of residue C in microbial communities, but residue type did not do so. Furthermore, residue C contributed more to PLFA-C pool in the LF than HF treatments, and the proportion of root C in PLFA-C pool was higher than that of shoot C, indicating easier immobilization of root C by soil microbial anabolism. Accordingly, soil fertility and residue quality could both regulate the kinetics of the microbial immobilization of crop residue C, but overall the available residual quantity of applied (plant-derived) C to enhance or maintain soil C pool did not depend on them in a long term in the agricultural Alfisols.

Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient.

Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH4). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO2) and CH4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.

Linking Microbial Community Composition in Treated Wastewater with Water Quality in Distribution Systems and Subsequent Health Effects.

The increases in per capita water consumption, coupled in part with global climate change have resulted in increased demands on available freshwater resources. Therefore, the availability of safe, pathogen-free drinking water is vital to public health. This need has resulted in global initiatives to develop sustainable urban water infrastructure for the treatment of wastewater for different purposes such as reuse water for irrigation, and advanced waste water purification systems for domestic water supply. In developed countries, most of the water goes through primary, secondary, and tertiary treatments combined with disinfectant, microfiltration (MF), reverse osmosis (RO), etc. to produce potable water. During this process the total bacterial load of the water at different stages of the treatment will decrease significantly from the source water. Microbial diversity and load may decrease by several orders of magnitude after microfiltration and reverse osmosis treatment and falling to almost non-detectable levels in some of the most managed wastewater treatment facilities. However, one thing in common with the different end users is that the water goes through massive distribution systems, and the pipes in the distribution lines may be contaminated with diverse microbes that inhabit these systems. In the main distribution lines, microbes survive within biofilms which may contain opportunistic pathogens. This review highlights the role of microbial community composition in the final effluent treated wastewater, biofilms formation in the distribution systems as the treated water goes through, and the subsequent health effects from potential pathogens associated with poorly treated water. We conclude by pointing out some basic steps that may be taken to reduce the accumulation of biofilms in the water distribution systems.

New insights into the role of microbial community composition in driving soil respiration rates

New insights into the role of microbial community composition in driving soil respiration rates

New insights into the role of microbial community composition in driving soil respiration rates

Microbial community plays critical roles in driving soil carbon (C) cycling in terrestrial ecosystems. However, we lack empirical evidence to demonstrate the role of microbial community in driving soil respiration - a key ecosystem process for global sustainability and climate regulation. Here, we used a long-term field experiment including multiple management practices, to identify, via statistical modeling, the role of microbial community composition in influencing soil respiration. We analyzed major soil properties and microbial (both bacterial and fungal) abundance, diversity and community composition. We found that different management regimes led to different soil respiration rates. Most importantly, microbial community composition explained a unique portion of the variation in soil respiration, which cannot be accounted for by key respiration drivers such as soil properties and other microbial attributes (richness and total abundance). Microbial biomass and fungal richness were also identified as key drivers of soil respiration. Our results indicate that inclusions of microbial compositional data in Earth system models can be potentially used to improve our capacity to predict changes in soil C balance under changing environments.

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

Methane dynamics regulated by microbial community response to permafrost thaw.

Permafrost contains about 50% of the global soil carbon. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ(13)C signature (10-15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus 'Methanoflorens stordalenmirensis' is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.

Microbial minorities modulate methane consumption through niche partitioning

Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating γ-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity-ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy.

The effect of a quorum-quenching enzyme on leaf litter decomposition

There is much interest in the role of microbial community composition in determining ecosystem processes but the role of interactions within these communities has often been underrepresented. One interaction within microbial communities is quorum-sensing, a type of density-dependent cell-to-cell communication. Here we examine the potential of quorum-sensing effects on litter decomposition in two communities (Forest and Meadow) by adding an enzyme that reduces quorum-sensing. The source of the community and quorum-sensing interacted to determine cumulative litter decomposition. Within the meadow community, enzyme additions caused no effect on decomposition, but in the forest community, inhibition of quorum-sensing resulted in a 14–17% decrease in decomposition. We suggest that quorum-sensing, a community interaction, may be an important determinant of litter decomposition in forested systems.

Microbial community composition and carbon cycling within soil microenvironments of conventional, low-input, and organic cropping systems.

This study coupled stable isotope probing with phospholipid fatty acid analysis ((13)C-PLFA) to describe the role of microbial community composition in the short-term processing (i.e., C incorporation into microbial biomass and/or deposition or respiration of C) of root- versus residue-C and, ultimately, in long-term C sequestration in conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato (Zea mays - Lycopersicum esculentum) cropping systems. During the maize growing season, we traced (13)C-labeled hairy vetch (Vicia dasycarpa) roots and residues into PLFAs extracted from soil microaggregates (53-250 μm) and silt-and-clay (<53 μm) particles. Total PLFA biomass was greatest in the organic (41.4 nmol g(-1) soil) and similar between the conventional and low-input systems (31.0 and 30.1 nmol g(-1) soil, respectively), with Gram-positive bacterial PLFA dominating the microbial communities in all systems. Although total PLFA-C derived from roots was over four times greater than from residues, relative distributions (mol%) of root- and residue-derived C into the microbial communities were not different among the three cropping systems. Additionally, neither the PLFA profiles nor the amount of root- and residue-C incorporation into the PLFAs of the microaggregates were consistently different when compared with the silt-and-clay particles. More fungal PLFA-C was measured, however, in microaggregates compared with silt-and-clay. The lack of differences between the mol% within the microbial communities of the cropping systems and between the PLFA-C in the microaggregates and the silt-and-clay may have been due to (i) insufficient differences in quality between roots and residues and/or (ii) the high N availability in these N-fertilized cropping systems that augmented the abilities of the microbial communities to process a wide range of substrate qualities. The main implications of this study are that (i) the greater short-term microbial processing of root- than residue-C can be a mechanistic explanation for the higher relative retention of root- over residue-C, but microbial community composition did not influence long-term C sequestration trends in the three cropping systems and (ii) in spite of the similarity between the microbial community profiles of the microaggregates and the silt-and-clay, more C was processed in the microaggregates by fungi, suggesting that the microaggregate is a relatively unique microenvironment for fungal activity.

Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest

To investigate the potential role of microbial community composition in soil carbon and nitrogen cycling, we transplanted soil cores between a grassland and a conifer ecosystem in the Sierra Nevada California and measured soil process rates (N-mineralization, nitrous oxide and carbondioxide flux, nitrification potential), soil water and temperature, and microbial community parameters (PLFA and substrate utilization profiles) over a 2 year period. Our goal was to assess whether microbial community composition could be related to soil process rates independent of soil temperature and water content. We performed multiple regression analyses using microbial community parameters and soil water and temperature as X-variables and soil process rates and inorganic N concentrations as Y-variables. We found that field soil temperature had the strongest relationship with CO2 production and soil NH4+ concentration, while microbial community characteristics correlated with N2O production, nitrification potential, gross N-mineralization, and soil NO3− concentration, independent of environmentalcontrollers. We observed a relationship between specific components of the microbial community (as determined by PLFA) and soil processes,particularly processes tightly linked to microbial phylogeny (e.g. nitrification). The most apparent change in microbial community composition in response to the 2 year transplant was a change in relative abundance of fungi (there was only one significant change in PLFA biomarkers for bacteria during 2 years). The relationship between microbial community composition and soil processes suggests that prediction of ecosystem response to environmental change may be improved by recognizing and accounting for changes in microbial community composition and physiological ecology.

The role of microbial community composition and groundwater chemistry in determining isoproturon degradation potential in UK aquifers

The community response of indigenous sandstone, chalk and limestone groundwater microorganisms to the addition of the commonly used herbicide isoproturon was examined. The addition of 100 μg l −1 isoproturon generally caused an increase in species diversity determined by chemotaxonomic analysis (fatty methyl ester analysis) of isolates resulting from incubation of cultures at 18 °C for 4 days. Amongst the groundwater samples to which isoproturon was added, isoproturon degradation rates were correlated with increasing dominance of a few species. However, the changes in community profile associated with isoproturon degradation varied from site to site. Repeated sub-culturing with 100 μg l −1 isoproturon and sterile groundwater was carried out to examine whether this level of pesticide could exert a selection pressure, and hence stimulate more rapid degradation. Significantly increased degradation was observed in a groundwater sample from the chalk, but not in sandstone, or limestone samples. The addition of filter-sterilised sandstone groundwater to bacteria on filter paper from slow degrading limestone sites significantly improved their degrading performance. The addition of filter-sterilised limestone groundwater to the sandstone bacteria reduced their degradation rate only slightly. The data suggested that the nature of the indigenous community does influence pesticide degradation in groundwater, but that the groundwater chemistry may also play a role.