Hydrological impacts on denitrification and nirS- and nirK- microbial community shifts in floodplains: Insights from water recession and flooding periods.

Knowledge on microbial community shifts during ecosystem succession from bare surfaces resulting from massive landscape stripping is extremely limited. Here we took advantage of an artificially created experimental catchment (6 ha) to assess structural and functional changes of microbial communities in ephemeral stream sediments and adjacent soils between 3 and 13 years after catchment construction. The catchment has since developed in undisturbed conditions, with major transformations in its morphology, hydrology and vegetation reflected by changes in microbial community structure and function. Initially dominated by cyanobacteria (42% of 16S rRNA reads in 2008 and 0.3% in 2018), the bacterial community shifted to an essentially heterotrophic composition within 10 years, when Alphaproteobacteria (12 vs 21%) and Planctomycetes (3 vs 16%), in particular, gained in importance. Similarly, Sordariomycetes (5% of ITS reads in 2008 and 27% in 2018) replaced Dothideomycetes (53 vs 14%) as the prevailing fungal class. Microbial respiration rates increased tenfold, from an average of 0.5–4.4 μg CO 2 g −1 DM h −1 , accompanied by an increase in potential enzyme activities. Seasonal patterns of microbial community functions were accentuated over a decade of catchment development, whereas structural community changes were less pronounced. Spatial variation of community composition also increased, with differences between soils and sediments intensifying over time. However, a striking disconnect between microbial community structure and function in 2008 had vanished by 2018. Thus, a decade of ecosystem succession resulted in fundamental shifts in microbial community structure and function, highlighting the intricate interplay between changing environmental conditions and microbial responses. • Re-connection of microbial community structure and function within a decade. • Shift in bacterial community composition from autotroph to heterotroph dominance. • Increased spatial heterogeneity of microbial communities during catchment succession. • Amplified seasonal variation in microbial function but not community structure.

We tested whether levels of soil available nitrogen (N) and phosphorus (P) control the composition and function of the soil microbial community in a Brown Chernozemic soil on the Canadian Prairie. Soil dissolved organic carbon, N and P, and microbial communities structure (phospholipid fatty acid profile) and function (enzyme activity) were evaluated in the fallow and first wheat (Triticum aestivum L. cv. AC Eatonia) phases of fallow-wheat-wheat rotations where the wheat received soil test recommended rates of mineral N and P fertilizers (+N+P), or where N (−N+P) or P (+N−P) fertilizer use was withheld for 37 years. Differential fertilization modified soil N and P availability, and microbial community structure. Low N level was a major constraint when a rapidly growing wheat crop (heading stage) was drawing on the resource, reducing both plant N uptake and soil microbial biomass-C in −N+P soils. Available P level in +N−P soils was about half that measured in P-fertilized soils, but P did not limit plant productivity or microbial development at that time. Changes in the microbial community structure seemingly buffered the impact of lower P availability in +N−P soils. Phosphatase activity was not involved, but increased abundance of arbuscular mycorrhizal fungi might be associated with this effect. Low soil N availability explained lower specific denitrification and higher specific nitrogenase activities in −N+P soil growing wheat. Higher denitrification activity in +N+P soil could be attributed to higher soil C level and fertilization-induced shifts observed in the structure of the soil microbial community. Irrespective of the fertility level of the soil, all microbial communities grew at the relative growth rate of 17% day−1 in a nutrient limitation assay that revealed no C, N or P limitation in these communities. We conclude that mineral fertilization, which modifies soil available N and P fertility, can be a selective force causing structural and functional shifts in the soil microbial community with a resulting impact on soil quality and nutrient fluxes.

Microbial mat communities consist of dense populations of microorganisms embedded in exopolymers and/or biomineralized solid phases, and are often found in mm-cm thick assemblages, which can be stratified due to environmental gradients such as light, oxygen or sulfide. Microbial mat communities are commonly observed under extreme environmental conditions, deriving energy primarily from light and/or reduced chemicals to drive autotrophic fixation of carbon dioxide. Microbial mat ecosystems are regarded as living analogues of primordial systems on Earth, and they often form perennial structures with conspicuous stratifications of microbial populations that can be studied in situ under stable conditions for many years. Consequently, microbial mat communities are ideal natural laboratories and represent excellent model systems for studying microbial community structure and function, microbial dynamics and interactions, and discovery of new microorganisms with novel metabolic pathways potentially useful in future industrial and/or medical applications. Due to their relative simplicity and organization, microbial mat communities are often excellent testing grounds for new technologies in microbiology including micro-sensor analysis, stable isotope methodology and modern genomics. Integrative studies of microbial mat communities that combine modern biogeochemical and molecular biological methods with traditional microbiology, macro-ecological approaches, and community network modeling will provide new and detailed insights regarding the systems biology of microbial mats and the complex interplay among individual populations and their physicochemical environment. These processes ultimately control the biogeochemical cycling of energy and/or nutrients in microbial systems. Similarities in microbial community function across different types of communities from highly disparate environments may provide a deeper basis for understanding microbial community dynamics and the ecological role of specific microbial populations. Approaches and concepts developed in highly-constrained, relatively stable natural communities may also provide insights useful for studying and understanding more complex microbial communities.

Shifts in microbial community and carbon sequestration in farmland soil under long-term conservation tillage and straw returning

Water use strategy of Carex cinerascens and its response to water condition changes in Poyang Lake Wetland, China

Experimental increases in pH and P availability exert long-term impacts on decomposition in forests

Microbial decomposition processes are typically described using first‐order kinetics, and the effect of elevated temperature is modeled as an increase in the rate constant. However, there is experimental data to suggest that temperature increases the pool size of substrate C available for microbial respiration with little effect on first‐order rate constants. We reasoned that changes in soil temperature alter the composition of microbial communities, wherein dominant populations at higher temperatures have the ability to metabolize substrates that are not used by members of the microbial community at lower temperatures. To gain insight into changes in microbial community composition and function following soil warming, we used molecular techniques of phospholipid fatty acid (PLFA) and lipopolysaccharide fatty acid (LPS‐OHFA) analysis and compared the kinetics of microbial respiration for soils incubated from 5 to 25°C. Substrate pools for microbial respiration and the abundance of PLFA and LPS‐OHFA biomarkers for Gram‐positive and Gram‐negative bacteria differed significantly among temperature treatments, providing evidence for a shift in the function and composition of microbial communities related to soil warming. We suggest that shifts in microbial community composition following either large seasonal variation in soil temperature or smaller annual increases associated with global climate change have the potential to alter patterns of soil organic matter decomposition by a mechanism that is not considered by current simulation models.

Permafrost, an important source of soil disturbance, is particularly vulnerable to climate change in Alaska where 85% of the land is underlained with discontinuous permafrost. Boreal forests, home to plants integral to subsistence diets of many Alaska Native communities, are not immune to the effects of climate change. Soil disturbance events, such as permafrost thaw, wildfires, and land use change can influence abiotic conditions, which can then affect active layer soil microbial communities. In a previous study, we found negative effects on boreal plants inoculated with microbes impacted by soil disturbance compared to plants inoculated with microbes from undisturbed soils. Here, we identify key shifts in microbial communities altered by soil disturbance using 16S rRNA gene sequencing and make connections between microbial community changes and previously observed plant growth. Additionally, we identify further community shifts in potential functional mechanisms using long read metagenomics. Across a soil disturbance gradient, microbial communities differ significantly based on the level of soil disturbance. Consistent with the earlier study, the family Acidobacteriaceae, which consists of known plant growth promoters, was abundant in undisturbed soil, but practically absent in most disturbed soil. In contrast, Comamonadaceae, a family with known agricultural pathogens, was overrepresented in most disturbed soil communities compared to undisturbed. Within our metagenomic data, we found that soil disturbance level is associated with differences in microbial community function, including mechanisms potentially involved in plant pathogenicity. These results indicate that a decrease in plant growth can be linked to changes in the microbial community and functional composition driven by soil disturbance and climate change. Together, these results build a genomic understanding of how shifting soil microbiomes may affect plant productivity and ecosystem health as the Arctic warms.

Deep exome resequencing is a powerful approach for delineating patterns of protein-coding variation among genes, pathways, individuals and populations.We analyzed exome data from 2,440 individuals of European and African ancestry as part of the National Heart, Lung, and Blood Institute's Exome Project, the aim of which is to discover novel genes and mechanisms that contribute to heart, lung and blood disorders.Each exome was sequenced to a mean coverage of 116×, allowing detailed inferences about the population genomic patterns of both common variation and rare coding variation.We identifi ed more than 500,000 single nucleotide variations, the majority of which were novel and rare (76% of variants had a minor allele frequency of less than 0.1%), refl ecting the recent dramatic increase in the size of the human population.The unprecedented magnitude of this dataset allowed us to rigorously characterize the large variation in nucleotide diversity among genes (ranging from 0 to 1.32%), as well as the role of positive and purifying selection in shaping patterns of proteincoding variation and the diff erential signatures of population structure from rare and common variation.This dataset provides a framework for personal genomics and is an important resource that will allow inferences of broad importance to human evolution and health.

Inadequate management of lignocellulosic waste poses a risk of substantial environmental pollution. Enriched microbial communities selected from environmental samples can effectively contribute to lignocellulose degradation. Utilizing a lower diversity but equally effective microbial community can enhance the control and efficiency of industrial operations. However, the mechanisms of cellulose degradation and functional microbial interactions within microbial communities with reduced diversity remain unclear. In this study, high-diversity and low-diversity lignocellulose-degrading communities were constructed using the dilution-to-stimulation and dilution-to-extinction methods. The enzymatic activity, community composition, degradation pathways, key functional microbes, and microbial co-occurrence network during cellulose degradation were analyzed in both high-diversity and low-diversity communities at the DNA and RNA level. Results showed that the low-diversity community exhibited a higher substrate degradation rate than the higher-diversity community. The activity of FPase and CMCase in the low-diversity community was significantly higher. Sphingobacterium, Pseudoxanthomonas, and Devosia were key players in the high-diversity community. Cellulomonas played a significant role in the low-diversity community. Reducing community diversity strengthens the cooperation among functional microbes. This study can guide the design of functional microbial synthetic communities and also can help to expand the ecological understanding of lignocellulosic waste degradation in synthetic microbial systems.IMPORTANCEMicrobial community diversity is pivotal in the degradation of lignocellulose. Nonetheless, reducing microbial diversity does not invariably result in decreased degradation efficiency. The utilization of low-diversity communities offers several advantages in industrial applications. Previous studies on lignocellulose-degrading functional microbial communities with low diversity have predominantly concentrated on community composition, with limited investigation into functionality and microbial interaction mechanisms. In this study, we constructed microbial communities with high and low diversity to investigate their efficiency in lignocellulose degradation and to elucidate the microbial ecological mechanisms. Our findings indicate that communities with low diversity decreased microbial competition and altered the composition of key functional microbes during the lignocellulose degradation process, thereby enhancing the efficiency of lignocellulose degradation. Investigating the microbial ecological mechanisms underlying lignocellulose degradation in both high- and low-diversity microbial communities can aid in the design of synthetic functional microbial communities and significantly contribute to the bioconversion of lignocellulosic waste.

The effects of environmental factors on water microbial communities have been extensively studied, but little is known about the effects in shrimp cultural enclosure ecosystems. We analyzed 16S rRNA gene amplicons to determine the principal environmental factors that shape the structure and function of microbial communities in shrimp cultural enclosure ecosystems from Guangdong and Hainan provinces, in China. High quality sequences were clustered into operational taxonomic units (OTUs) at the 97% similarity level, generating 659–1,835 OTUs per sample. The 10 most abundant phyla were Proteobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Firmicutes, Chlorobi, Chloroflexi, and Chlamydiae. The results of canonical correspondence analyses (CCA) indicated that salinity, total phosphate (TP), total nitrogen (TN), temperature, and pH were the most important factors shaping microbial community structure. Differences in microbial community structure between high and low salinity samples were explained by changes in the relative abundances of some OTUs (e.g., OTU5, OTU19, OTU21, OTU39, and OTU71). Moreover, the contribution of spatial distribution to the microbial community assembly was investigated via aggregated boosted tree (ABT) analyses, and the results indicated spatial isolation was not a major factor affecting the phylogenetic diversity and phylotypes of water microbial communities. Furthermore, we predicted water microbial community functional profiling using the PICRUSt program and principal component analyses (PCA) suggested that salinity was a major contributor to the structure and function of the microbial communities. Collectively, these results showed that environmental factors influenced the structure and function of water microbial communities, while salinity was the principal environmental factor instead of temperature, TP, TN, and pH in shrimp cultural enclosure ecosystems.

Soil carbon and nitrogen dynamics affect bacterial and fungal communities and their interactions: a review

Soil microorganisms are key regulators of soil carbon (C) and nutrients cycles in terrestrial ecosystems. However, it remains uncertain how the inter-annual variation in soil microbial community corresponds well with resource availability in the changing environment. Here, we investigated soil microbial community structure and abundance, as well as the associated environmental variables from 2015 to 2017 under different plant detritus input manipulation treatments in a coniferous (Platycladus orientalis (Linn.) Franco) plantation forest ecosystem in subtropical China. Our results showed that the inter-annual variation in soil microbial community was more visible than that caused by detritus input manipulations, owing to the temporal alterations in microclimates and substrate availability. Both aboveground litter removal and root exclusion had more negative effects on the bacterial PLFAs than fungi except half a year after detritus input manipulations. While, soil microbial abundance increased only after three years of litter addition compared to control. Litter removal, especially the no input treatment significantly increased the fungi to bacteria (F:B) and Gram-positive to Gram-negative bacteria (GP:GN) ratios after one and two years of detritus input manipulations. Whereas, the litter addition treatment had minor effects on these parameters. A clear discrimination of microbial community structure among the different detritus input manipulations appeared after two and three years. Both the F:B and GP:GN ratios were positively related to the carbon to nitrogen (C:N) ratio, recalcitrance index of carbon (RIC) and nitrogen (RIN). Overall, our results reveal that the inter-annual variations in soil microbial community are clearly differentiated by the environmental variables and substrate availability that occur in different years and detritus input manipulations. Our results also suggest that due to the vital role of microorganisms in biogeochemical cycling, shifts in the microbial community structure with altered plant detritus input could profoundly affect ecosystem processes in the long run.

We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.IMPORTANCE We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.

Subsurface microbial communities mediate the transformation and fate of redox sensitive materials including organic matter, metals and radionuclides. Few studies have explored how changing geochemical conditions influence the composition of groundwater microbial communities over time. We temporally monitored alterations in abiotic forces on microbial community structure using 1L in-field bioreactors receiving background and contaminated groundwater at the Oak Ridge Reservation, TN. Planktonic and biofilm microbial communities were initialized with background water for 4 days to establish communities in triplicate control reactors and triplicate test reactors and then fed filtered water for 14 days. On day 18, three reactors were switched to receive filtered groundwater from a contaminated well, enriched in total dissolved solids relative to the background site, particularly chloride, nitrate, uranium, and sulfate. Biological and geochemical data were collected throughout the experiment, including planktonic and biofilm DNA for 16S rRNA amplicon sequencing, cell counts, total protein, anions, cations, trace metals, organic acids, bicarbonate, pH, Eh, DO, and conductivity. We observed significant shifts in both planktonic and biofilm microbial communities receiving contaminated water. This included a loss of rare taxa, especially amongst members of the Bacteroidetes, Acidobacteria, Chloroflexi, and Betaproteobacteria, but enrichment in the Fe- and nitrate- reducing Ferribacterium and parasitic Bdellovibrio. These shifted communities were more similar to the contaminated well community, suggesting that geochemical forces substantially influence microbial community diversity and structure. These influences can only be captured through such comprehensive temporal studies, which also enable more robust and accurate predictive models to be developed.