Heterogeneity Of Microbial Communities Research Articles

High-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics.

Metaproteomics offers a direct avenue to identify microbial proteins in microbiota, enabling the compositional and functional characterization of microbiota. Due to the complexity and heterogeneity of microbial communities, in-depth and accurate metaproteomics faces tremendous limitations. One challenge in metaproteomics is the construction of a suitable protein sequence database to interpret the highly complex metaproteomic data, especially in the absence of metagenomic sequencing data. Herein, we present a high-abundance protein-guided hybrid spectral library strategy for in-depth data independent acquisition (DIA) metaproteomic analysis (HAPs-hyblibDIA). A dedicated high-abundance protein database of gut microbial species is constructed and used to mine the taxonomic information on microbiota samples. Then, a sample-specific protein sequence database is built based on the taxonomic information using Uniprot protein sequence for subsequent analysis of the DIA data using hybrid spectral library-based DIA analysis. We evaluated the accuracy and sensitivity of the method using synthetic microbial community samples and human gut microbiome samples. It was demonstrated that the strategy can successfully identify taxonomic compositions of microbiota samples and that the peptides identified by HAPs-hyblibDIA overlapped greatly with the peptides identified using a metagenomic sequencing-derived database. At the peptide and species level, our results can serve as a complement to the results obtained using a metagenomic sequencing-derived database. Furthermore, we validated the applicability of the HAPs-hyblibDIA strategy in a cohort of human gut microbiota samples of colorectal cancer patients and controls, highlighting its usability in biomedical research.

Insights into the composition and assembly mechanism of microbial communities on intertidal microsand grains

IntroductionMarine microorganisms are essential in marine ecosystems and have always been of interest. Currently, most marine microbial communities are studied at the bulk scale (millimeters to centimeters), and the composition, function and underlying assembly mechanism of microbial communities at the microscale (sub-100 micrometers) are unclear.MethodsThe microbial communities on microsand grains (40–100 µm, n = 150) from marine sediment were investigated and compared with those on macrosand grains (400–1000 µm, n = 60) and bulk sediments (n = 5) using amplicon sequencing technology.ResultsThe results revealed a significant difference between microsand grains and macrosand grains. Microsand grains had lower numbers of operational taxonomic units (OTUs(97%)) and predicted functional genes than macrosand grains and bulk-scale samples. Microsand grains also showed greater intersample differences in the community composition and predicted functional genes than macrosand grains, suggesting a high level of heterogeneity of microbial communities at the microscale. Analyses based on ecological models indicated that stochastic processes dominated the assembly of microbial communities on sand grains. Consistently, cooccurrence network analyses showed that most microbial cooccurrence associations on sand grains were highly unstable. Metagenomic sequencing and further genome-scale metabolic modeling revealed that only a small number (1.3%) of microbe pairs showed high cooperative potential.DiscussionThis study explored the microbial community of marine sediments at the sub-100 µm scale, broadening the knowledge of the structure and assembly mechanism of marine microbial communities.

Decoupling the heterogeneity of sediment microbial communities along the urbanization gradients: A Bayesian-based approach

Comprehending the response of microbial communities in rivers along urbanization gradients to hydrologic characteristics and pollution sources is critical for effective watershed management. However, the effects of complex factors on riverine microbial communities remain poorly understood. Thus, we established a bacteria-based index of biotic integrity (Ba-IBI) to evaluate the microbial community heterogeneity of rivers along an urbanization gradient. To examine the response of Ba-IBI to multiple stressors, we employed a Bayesian network based on structural equation modeling (SEM-BN) and revealed the key control factors influencing Ba-IBI at different levels of urbanization. Our findings highlight that waterborne nutrients have the most significant direct impact on Ba-IBI (r = −0.563), with a particular emphasis on ammonia nitrogen, which emerged as the primary driver of microbial community heterogeneity in the Liuyang River basin. In addition, our study confirmed the substantial adverse effects of urbanization on river ecology, as urban land use had the greatest indirect effect on Ba-IBI (r = −0.460). Specifically, the discharge load from wastewater treatment plants (WWTP) was found to significantly negatively affect the Ba-IBI of the entire watershed. In the low urbanized watersheds, rice cultivation (RC) and concentrated animal feeding operations (CAFO) are key control factors, and an increase in their emissions can lead to a sharp decrease in Ba-IBI. In moderately urbanized watersheds, the Ba-IBI tended to decrease as the level of RC emissions increased, while in those with moderate RC emissions, an increase in point source emissions mitigated the negative impact of RC on Ba-IBI. In highly urbanized watersheds, Ba-IBI was not sensitive to changes in stressors. Overall, our study presents a novel approach by integrating Ba-IBI with multi-scenario analysis tools to assess the effects of multiple stressors on microbial communities in river sediments, providing valuable insights for more refined environmental decision-making.

Effects of a long-term operation wetland for wastewater treatment on the spatial pattern and function of microbial communities in groundwater

Constructed wetlands have been used globally for wastewater treatment owing to low energy inputs and operating costs. However, the impact of their long-term operation on groundwater microbial communities is still unclear. This study aims to investigate the effects and further reveal the linkage between a large-scale surface flow constructed wetland (in operation for 14 years) and groundwater. Changes in the characteristics of groundwater microbial communities and their potential influencing factors were studied based on hydrochemical analysis, Illumina MiSeq sequencing, and multivariate statistical analysis methods. Results show that the long-term operation wetland significantly elevated groundwater nutrient levels and increased the risk of ammonia nitrogen pollution compared to background values. An apparent heterogeneity of microbial communities exhibited in the vertical direction and a similarity in the horizontal direction. Wetland operations substantially altered the structure of microbial communities at 3, 5, and 12 m depths, particularly a reduced abundance of denitrifying and chemoheterotrophic functional genera. The formation and evolution of groundwater microbial community structure mainly subjected to the contributions of dissolved oxygen (33.70%), total nitrogen (21.40%), dissolved organic carbon (11.09%), and pH (10.60%) variations resulted from the wetland operation and largely differed in depths. A combined effect of these factors on the groundwater should be concerned for such a long-term running wetland system. This study provides a new insight into the responses of groundwater microbial community structure driving by wetland operation and a better understanding of corresponding variation of microbial-based geochemical processes.

Interspecific and intraspecific Taylor's laws for frog skin microbes

Amphibians are known to have an abundance of microorganisms colonizing their skin, and these symbionts often protect the host from disease. There are now many comprehensive studies on amphibian skin microbes, but the interspecific and intraspecific abundance distributions (or abundance heterogeneity) of amphibian skin microbes remain unclear. Furthermore, we have a very limited understanding of how the abundance and heterogeneity of microbial communities relate to the body size (or more specifically, skin surface area) of amphibian hosts. In this study, we evaluated the interspecific and intraspecific abundance distribution patterns of amphibian skin microbes and evaluated whether the symbiotic skin microbes of different anuran species share a fundamental heterogeneity scaling parameter. If scaling invariance exists, we hypothesize that a fundamental heterogeneity scaling value also exists. A total of 358 specimens of 10 amphibian host species were collected, and we used Type-I and III Taylor’s power law expansions (TPLE) to assess amphibian skin microbial heterogeneity at the community and mixed-species population levels, respectively. The obtained results showed that, at the community scale, a high aggregation of the microbial abundance distribution on the skin barely changed with host size. In a mixed-species population (i.e., a community context), the abundance distribution pattern of mixed microbial species populations also does not change with host size and always remains highly aggregated. These findings suggest that while amphibian skin microbiomes located in different hosts may have different environmental conditions, they share a fundamental heterogeneity scaling parameter, and thus, scale invariance exists. Finally, we found that microhabitat area provided by the host skin is vital to the stability of the symbiotic microbial community.

Vertically co-distributed vanadium and microplastics drive distinct microbial community composition and assembly in soil

Vanadium (V) and microplastics in soils draw increasing attention considering their significant threats to ecosystems. However, little is known about the vertical co-distribution of V and microplastics in soil profile and their combined effects on microbial community dynamics and assembly. This study investigated the spatial distribution of V and microplastics in the soils at a V smelting site and the associated microbial community characteristics along the vertical gradient. Both V and microplastics were found in the 50 cm soil profile with average concentrations of 203.5 ± 314.4 mg/kg and 165.1 ± 124.8 item/kg, respectively. Topsoil (0–20 cm) and subsoil (20–50 cm) displayed distinct microbial community compositions. Metal-tolerant (e.g., Spirochaeta, Rubellimicrobium) and organic-degrading (e.g., Bradyrhizobium, Pseudolabrys) taxa as biomarkers were more abundant in the topsoil layer. V and microplastics directly affected the microbial structure in the topsoil and had indirect influences in the subsoil, with direct impacts from organic matter. In topsoil, deterministic processes were more prevalent for community assembly, whereas stochastic processes governed the subsoil. The interspecific relationship was closer in topsoil with greater network complexity and higher modularity. These findings promote the understanding of distinct heterogeneity of microbial communities jointly driven by V and microplastics in soil environment.

Microbial Diversity in Groundwater and Its Response to Seawater Intrusion in Beihai City, Southern China.

Seawater intrusion is a major concern commonly found in coastal aquifers worldwide. Because of the intense aquifer exploitation and land-based marine aquaculture in the coastal area of Beihai City, Guangxi Zhuang Autonomous Region, China, numerous underground aquifers in this area have been affected by seawater intrusion. However, the microbial communities in freshwater aquifers and their response to seawater intrusion are still unclear. In this study, groundwater from three aquifers was collected from three monitoring sites at different distances from the coastline in the coastal area of Beihai City, and the hydrochemical characteristics of these groundwater samples and the structure of the associated microbial communities were analyzed. The Cl− concentration of the samples indicated that seawater intrusion had occurred in the research area up to 1.5 km away from the coastline, but the monitoring site 2 km away from the coastline had yet to be affected. Statistical analysis showed that the bacterial communities in different groundwater aquifers were significantly correlated with the Cl− concentration, thereby suggesting that the extent of seawater intrusion might be one of the primary factors shaping bacterial composition in groundwater of this area, but the composition and distribution of archaea did not show a significant response to seawater intrusion and presented no apparent correlation with the Cl− concentration. α-, γ-Proteobacteria and Bacteroidota were the dominant bacterial lineages, accounting for about 58–95% of the bacterial communities. Meanwhile, the predominant archaeal taxa were mainly composed of Crenarchaeota, Nanoarchaeota, and Thermoplasmatota, as accounting for 83–100%. Moreover, there was significant spatial heterogeneity of microbial communities in the aquifers affected by varying degrees of seawater intrusion. The microbial communities inhabiting the unconfined aquifer were influenced by the geochemical fluctuation caused by seawater infiltration from land-based marine aquaculture ponds and the diffusion of eutrophic surface water. In contrast, changes in microbial community structure in the confined aquifers were closely related to the environmental gradient caused by different degrees of seawater intrusion. In addition, we also found that the tidal cycle did not significantly affect the structure of microbial communities inhabiting confined aquifers that had been long affected by seawater intrusion.

Morphological and Spatial Heterogeneity of Microbial Communities in Pilot-Scale Autotrophic Integrated Fixed-Film Activated Sludge System Treating Coal to Ethylene Glycol Wastewater.

The understanding of microbial compositions in different dimensions is essential to achieve the successful design and operation of the partial nitritation/anammox (PN/A) process. This study investigated the microbial communities of different sludge morphologies and spatial distribution in the one-stage PN/A process of treating real coal to ethylene glycol (CtEG) wastewater at a pilot-scale integrated fixed-film activated sludge (IFAS) reactor. The results showed that ammonia-oxidizing bacteria (AOB) was mainly distributed in flocs (13.56 ± 3.16%), whereas anammox bacteria (AnAOB) was dominated in the biofilms (17.88 ± 8.05%). Furthermore, the dominant AnAOB genus in biofilms among the first three chambers was Candidatus Brocadia (6.46 ± 2.14% to 11.82 ± 6.33%), whereas it was unexpectedly transformed to Candidatus Kuenenia (9.47 ± 1.70%) and Candidatus Anammoxoglobus (8.56 ± 4.69%) in the last chamber. This demonstrated that the niche differentiation resulting from morphological (dissolved oxygen) and spatial heterogeneity (gradient distribution of nutrients and toxins) was the main reason for dominant bacterial distribution. Overall, this study presents more comprehensive information on the heterogeneous distribution and transformation of communities in PN/A processes, providing a theoretical basis for targeted culture and selection of microbial communities in practical engineering.

Importance of microbial communities at the root-soil interface for extracellular polymeric substances and soil aggregation in semiarid grasslands

In the past years, extracellular polymeric substances (EPS) produced by soil microorganisms received an increasing interest, as they not only protect microbes against environmental stresses, but seem to play a pivotal role in soil structure formation as well. Within soils, root deposits provide an important source of easily accessible energy and nutrients, stimulating microbial growth to produce EPS. Especially under semiarid climates, where a full vegetation cover cannot be sustained, large gradients in living conditions for microbes can be found between the root-soil interface and barren intercanopy spaces.In this study, we aimed to elucidate the plant-specific effects on microbes, EPS production and soil aggregation. At two sites in southern Spain, differing in carbonate and graphite content, legume shrubs of Anthyllis cytisoides and grass tussocks of Macrochloa tenacissima were selected. Soil samples were taken in the adjacent bare interspace, under the canopy and of the rhizosphere. From these samples the microbial community (here bacteria and archaea), EPS(-saccharide) content and soil aggregation (<1 mm) were analysed. DNA extracted from the microbial cells detached from the surface of the sampled roots (rhizoplane), was subjected to 16S rRNA gene amplicon sequencing.The rhizoplane microbial communities differed strongly between plant species and sites, whereby site was the most important factor shaping the communities. The plant species effect on microbial communities diminished strongly with distance to the root surface. At the carbonate-poor Rambla Honda site (site 1), plant species-specific effects were observed in the rhizoplane and rhizosphere, whereas in the carbonate-rich Alboloduy site (site 2) almost no plant species-specific effects were found at the genus level. The larger heterogeneity in microbial communities at site 1 was reflected in EPS-saccharide contents and subsequent soil aggregation, while no difference in soil aggregation was found at site 2. Both parameters increased strongest in the Anthyllis cytisoides rhizosphere at site 1.Despite the lack of a strong gradient with distance from the root at the carbonate-rich site 2, microbial taxa were found by network analysis that positively correlated to EPS-saccharide contents and/or soil aggregation. The relationship between the identified taxa and EPS and/or aggregation relationships were clearest at the root-soil interface, while several other taxa were found to be widely occurring in the other soil compartments too.In conclusion, we found in all compartments potential EPS producers, which could have influenced soil aggregation. Nevertheless, microbes with higher relative abundance in the rhizoplane were linked to higher EPS contents, especially in conjunction with legume shrubs, and subsequently related to soil aggregation. The spatial extent of the root effect was only governed by carbonate contents, as higher carbonate content diminished the observed root effects on the microbial community and subsequent soil aggregation.

Heterogeneity of Microbial Communities in Soils From the Antarctic Peninsula Region.

Ice-free areas represent less than 1% of the Antarctic surface. However, climate change models predict a significant increase in temperatures in the coming decades, triggering a relevant reduction of the ice-covered surface. Microorganisms, adapted to the extreme and fluctuating conditions, are the dominant biota. In this article we analyze the diversity and composition of soil bacterial communities in 52 soil samples on three scales: (i) fine scale, where we compare the differences in the microbial community between top-stratum soils (0–2 cm) and deeper-stratum soils (5–10 cm) at the same sampling point; (ii) medium scale, in which we compare the composition of the microbial community of top-stratum soils from different sampling points within the same sampling location; and (iii) coarse scale, where we compare communities between comparable ecosystems located hundreds of kilometers apart along the Antarctic Peninsula. The results suggest that in ice-free soils exposed for longer periods of time (millennia) microbial communities are significantly different along the soil profiles. However, in recently (decades) deglaciated soils the communities are not different along the soil profile. Furthermore, the microbial communities found in soils at the different sampling locations show a high degree of heterogeneity, with a relevant proportion of unique amplicon sequence variants (ASV) that appeared mainly in low abundance, and only at a single sampling location. The Core90 community, defined as the ASVs shared by 90% of the soils from the 4 sampling locations, was composed of 26 ASVs, representing a small percentage of the total sequences. Nevertheless, the taxonomic composition of the Core80 (ASVs shared by 80% of sampling points per location) of the different sampling locations, was very similar, as they were mostly defined by 20 common taxa, representing up to 75.7% of the sequences of the Core80 communities, suggesting a greater homogeneity of soil bacterial taxa among distant locations.

Microbial Community Heterogeneity Within Colorectal Neoplasia and its Correlation With Colorectal Carcinogenesis

Gut microbial dysbiosis has pivotal involvement in colorectal cancer (CRC). However, the intratumoral microbiota and its association with CRC progression remain elusive. We aimed to determine the microbial community architecture within a neoplasia (CRC or adenoma) and its contribution to colorectal carcinogenesis. We collected 436 tissue biopsies from patients with CRC (n= 36) or adenoma (n= 32) (2-6 biopsies from a neoplasia plus 2-5 biopsies from adjacent normal tissues per individual). Microbial profiling was performed using 16S ribosomal RNA gene sequencing with subsequent investigation of microbiota diversities and heterogeneity. The correlation between microbial dysbiosis and host genetic alterations (KRAS mutation and microsatellite instability) in all neoplasia biopsies was also analyzed. We discovered that intra-neoplasia microbial communities are heterogeneous. Abundances of some CRC-associated pathobionts (eg, Fusobacterium, Bacteroides, Parvimonas, and Prevotella) were found to be highly varied within a single neoplasia. Correlation of such heterogeneity with CRC development revealed alterations in microbial communities involving microbes with high intra-neoplasia variation in abundance. Moreover, we found that the intra-neoplasia variation in abundance of individual microbes changed along the adenoma-carcinoma sequence. We further determined that there was a significant difference in intra-neoplasia microbiota between biopsies with and without KRAS mutation (P < .001) or microsatellite instability (P < .001), and illustrated the association of intratumoral microbial heterogeneity with genetic alteration. We demonstrated that intra-neoplasia microbiota is heterogeneous and correlated with colorectal carcinogenesis. Our findings provide new insights on the contribution of gut microbiota heterogeneity to CRC progression.

Environmental Factors Driving Spatial Heterogeneity in Desert Halophile Microbial Communities.

Spatial heterogeneity in microbial communities is observed in all natural ecosystems and can stem from both adaptations to local environmental conditions as well as stochastic processes. Extremophile microbial communities inhabiting evaporitic halite nodules (salt rocks) in the Atacama Desert, Chile, are a good model ecosystem for investigating factors leading to microbiome heterogeneity, due to their diverse taxonomic composition and the spatial segregation of individual nodules. We investigated the abiotic factors governing microbiome composition across different spatial scales, allowing for insight into the factors that govern halite colonization from regional desert-wide scales to micro-scales within individual nodules. We found that water availability and community drift account for microbiome assembly differently at different distance scales, with higher rates of cell dispersion at the smaller scales resulting in a more homogenous composition. This trend likely applies to other endoliths, and to non-desert communities, where dispersion between communities is limited. At the intra-nodule scales, a light availability gradient was most important in determining the distribution of microbial taxa despite intermixing by water displacement via capillary action.

Comparing microbial community heterogeneity in soil under organic and conventional agricultural system cultivated with olive and peach trees in three fields differ with age at Al-Jouf Saudi Arabia

Comparing microbial community heterogeneity in soil under organic and conventional agricultural system cultivated with olive and peach trees in three fields differ with age at Al-Jouf Saudi Arabia

Comparing microbial community heterogeneity in soil under organic and conventional agricultural system cultivated with olive and peach trees in three fields differ with age at Al-Jouf Saudi Arabia

This research study was carried out at Al-Jouf region, north eastern Saudi Arabia, to investigate the differences in microbial community and density of microorganisms in the rhizosphere of olive (Olea europaea) and peach (Prunus persica) tree fields subjected to growth under organic and conventional agriculture systems. The soil analytical processes were conducted in three olive and three peach fields (9, 17, 27 years old and 20 ha in area) under organic fertilization, and three similar olive and peach fields under conventional fertilization system. The results indicated significant variations between the two agricultural systems in rhizosphere content of microbial and mycorrhizal colonization%. The highest percentages of actinomycetes, total fungi and bacteria (PSM) were recorded in the organically agricultural system (OAS) in olive fields in comparison to conventionally agricultural system (CAS). Regarding field ages OAS dominated CAS in total number of fungi under all olive fields ages, while under peach fields fungi counts were significantly high under CAS compared to OAS. Under peach fields OAS dominated giving the highest actinomycetes and bacteria and CAS dominated by giving the highest CFU and fungi count. The significantly highest counts of CFU and bacteria were attained under conventional farming system (CAS) in all of the different aged field compared to OAS. Actinomycetes and bacteria in young fields were significantly high under CAS, while in old fields actinomycetes and fungi counts were the highest under OAS.

History of petroleum disturbance triggering the depth-resolved assembly process of microbial communities in the vadose zone

Biogeochemical gradient forms in vadose zone, yet little is known about the assembly processes of microbial communities in this zone under petroleum disturbance. This study collected vadose zone soils at three sites with 0, 5, and 30 years of petroleum contamination to unravel the vertical microbial community successions and their assembly mechanisms. The results showed that petroleum hydrocarbons exhibited higher concentrations at the long-term contaminated site, showing negative impacts on some soil properties, retarding in the surface soils and decreasing along soil depth. Cultivable fraction of heterotrophic bacteria and microbial α-diversity decreased along depth in vadose zones with short-term/no contamination history, but exhibited an opposite trend with long-term contamination history. Petroleum contamination intensified the vertical heterogeneity of microbial communities based on the contamination time. Microbial co-occurrence network revealed the lowest species co-occurrence pattern at the long-term contaminated site. The distance-decay patterns and null model analysis together suggested distinct assembly mechanisms at three sites, where dispersal limitation (42–45%) was higher and variable and homogenizing selections were lower (37–38%) in vadose zones under petroleum disturbance than those in the uncontaminated vadose zone. Our findings help to better understand the subsurface biogeochemical cycles and bioremediation of petroleum-contaminated vadose zones.

Temporal heterogeneity of microbial communities and metabolic activities during a natural algal bloom

Elucidating the interactions between algae and associated microbial communities is critical for understanding the mechanisms that mediate the dynamic of harmful algal blooms (HABs) in marine environment. However, the microbial functional profiles and their biogeochemical potential in HABs process remains elusive, especially during a complete natural HAB cycle. Here, we used pyrosequencing and functional gene array (GeoChip) to investigate microbial community dynamics and metabolic potential during a natural dinoflagellate (Noctiluca scintillans) bloom. The results shown that bacterioplankton exhibited significant temporal heterogeneity over the course of the bloom stages. Microbial succession was co-driven by environmental parameters and biotic interactions. The functional analysis revealed significant variations in microbial metabolism during matter cycling. At bloom onset-stage, metabolic potential associated with iron oxidation and transport was elevated. Carbon fixation and degradation, denitrification, phosphorus acquisition, and sulfur transfer/oxidation were significantly enhanced at the plateau stage. During the decline and terminal stages, oxidative stress, lysis of compounds, and toxin degradation & protease synthesis increased. This work reveal phycosphere microorganisms can enhanced organic C decomposition capacity, altered N assimilation rate and S/P turnover efficiency, and balancing of the Fe budget during HAB process. The ecological linkage analysis has further shown that microbial composition and functional potential were significantly linked to algal blooms occurrence. It suggest that structural variability and functional plasticity of microbial communities influence HAB trajectory.

Estimating the Optimum Coverage and Quality of Amplicon Sequencing With Taylor's Power Law Extensions.

Theoretical analysis of DNA sequencing coverage problem has been investigated with complex mathematical models such as Lander–Waterman expectation theory and Stevens’ theorem for randomly covering a domain. In the field of metagenomics sequencing, several approaches have been developed to estimate the coverage of whole-genome shotgun sequencing, but surprisingly few studies addressed the coverage problem for marker-gene amplicon sequencing, for which arguably the biggest challenge is the complexity or heterogeneity of microbial communities. Overall, much of the practice still relies variously on speculation, semi-empirical and ad hoc heuristic models. Conservatively raising coverage may ensure the success of sequencing project, but often with unduly cost. In this study, we borrow the principles and approaches of optimum sampling methodology originated in applied entomology, achieved equal success in plant pathology and parasitology, and plays a critical role in the decision-making for global crop and forest protection against economic pests since 1970s when the pesticide crisis and food safety concerns forced the reduction of pesticide usages, which in turn requires reliable sampling techniques for monitoring pest populations. We realized that sequencing coverage is essentially an optimum sampling problem. Perhaps the only essential difference between sampling insects and sampling microbiome is the “instrument” used. In traditional entomology, it is usually humans that visually count the numbers of insects, occasionally aided by binocular microscope. In the metagenomics research, it is the DNA sequencers that count the number of DNA reads. Furthermore, a key theoretical foundation for sampling insect pest populations, i.e., Taylor’s power law, which achieved rare status of ecological law and captures the population aggregation, has been recently extended to the community level for describing community heterogeneity and stability, namely, Taylor’s power law extensions (TPLEs). This theoretical advance enabled us to develop a novel approach to assessing the quality and determining optimum reads (coverage) of amplicon sequencing operations. Specifically, two applications were developed: one is, in hindsight, to assess the quality of amplicon sequencing operation in terms of the precision and confidence levels. Another is, prior to sequencing operation, to determine the minimum sequencing efforts for a sequencing project to achieve preset precision and confidence levels.

Interrogation of Internal Workings in Microbial Community Assembly: Play a Game through a Behavioral Network?

Increasing evidence shows that the influence of microbiota on biogeochemical cycling, plant development, and human health is executed through a complex network of microbe-microbe interactions. However, characterizing how microbes interact and work together within closely packed and highly heterogeneous microbial ecosystems is extremely challenging. Here, we describe a rule-of-thumb framework for visualizing polymicrobial interactions and extracting general principles that underlie microbial communities. We integrate elements of metabolic ecology, behavioral ecology, and game theory to quantify the interactive strategies by which microbes at any taxonomic level compete for resources and cooperate symbiotically with each other to form and stabilize ecological communities. We show how the framework can chart an omnidirectional landscape of microbial cooperation and competition that may drive various natural processes. This framework can be implemented into genome-wide association studies to unravel the genetic mechanisms underlying microbial interaction networks and their evolutionary consequences along spatiotemporal gradients.IMPORTANCE Identifying general biological rules that underlie the complexity and heterogeneity of microbial communities has proven to be highly challenging. We present a rule-of-thumb framework for studying and characterizing how microbes interact with each other across different taxa to determine community behavior and dynamics. This framework is computationally simple but conceptually meaningful, and it can provide a starting point to generate novel biological hypotheses about microbial interactions and explore internal workings of microbial community assembly in depth.

Grazing Regulates the Spatial Heterogeneity of Soil Microbial Communities Within Ecological Networks

Grazing is a major driver of the composition of microbial communities, which play important roles in soil functioning. Mechanisms whereby grazing might regulate the spatial heterogeneity of microbial communities within ecological networks remain largely untested. We used network analysis to identify the impacts of increasing grazing intensity by livestock (cattle, sheep, goats), and native (kangaroos) and wild (rabbits) animals, on the spatial heterogeneity of the relative abundance of eight ecological clusters of co-occurring soil microbial taxa: four from Grasslands and four from Forests. Grazing effects on microbial spatial heterogeneity were strongly nuanced and depended on (1) plant community type, (2) herbivore type and (3) microbial identity. Microbial within-site spatial heterogeneity was greater in Grasslands than in Forests, and most effects of grazing on microbial spatial heterogeneity were in Forests, effecting three of the four Forest clusters, but only one Grassland cluster. The associations between grazing intensity and microbial heterogeneity were driven indirectly by changes in the spatial heterogeneity of litter cover and soil pH. For Grasslands, we also detected a direct effect of grazing intensity on the heterogeneity of particular microbial groups. Our results indicate that increased grazing intensity will advantage some microbial clusters but disadvantage others. Together, our study provides evidence that grazing intensity regulates the abundance and spatial heterogeneity of microbial communities within ecological networks. Knowing the potential effects of herbivores on different microbial clusters can help us predict the likely effects of grazing on soil function. This has important implications for future sustainable management and conservation policies.

Spatial variation in soil microbial community structure and its relation to plant distribution and local environments following afforestation in central China

Land use change directly influences soil microbial communities by altering vegetation cover. However, how soil microbial community structure responds spatially to plant distribution within a land use type following afforestation remains unclear. Here, we investigated the spatial variations in soil microbial biomass [e.g., bacteria (B), fungi (F), gram-positive bacteria (G+), and gram-negative bacteria (G−)] and community composition (the F:B ratio and G+:G- ratio) in woodland, shrubland and adjacent open areas (i.e., control) in the Danjiangkou Reservoir of central China, using geostatistical methods and phospholipid fatty acid (PLFA) analysis. We also explored the underlying mechanisms of whether or not and how environmental drivers, including biotic factors (e.g., tree distribution, present litter and root biomass) and abiotic factors [e.g., soil organic carbon (SOC) and total nitrogen (TN), soil pH, and soil moisture], regulated the spatial variations in these microbial properties using partial Mantel tests. Afforestation increased the PLFA content and the G+:G- ratio but reduced the F:B ratio compared to that of the open area. Spatial analysis revealed that spatial variations in microbial communities were governed by local environmental drivers affected by tree distribution. Generally, SOC was a critical control on microbial biomass and community composition in all land use types, but the major drivers varied with land use type. Soil pH, SOC and TN affected almost all types of microbial PLFAs in shrubland, whereas litter biomass, SOC and TN were selectively correlated with specific groups of PLFAs (mainly from bacteria) in woodland. Soil pH affected the F:B ratio rather than the G+:G- ratio in both woodland and shrubland, while root biomass, SOC and TN were proved to be determinants of the F:B ratio and G+:G- ratio in shrubland. Other than SOC, the soil pH and N level were the primary controls on spatial variations in microbial biomass following afforestation. Overall, our results revealed that tree distribution-induced shifts in local environments controlled the spatial variations in soil microbial community structure within one land use type, highlighting that the role of spatial heterogeneity in microbial communities has important implications for land management.