Microbial Community Assembly Patterns Research Articles

Revealing microbial community assembly patterns and succession process in the blackening process of black-odor water

Human-imported pollutants could induce water black, changing microbial community structure and function. Employed 16S rRNA high-throughput sequencing, field-scale investigations and laboratory-scale experiments were successively conducted to reveal mechanistic insights into microbial community assembly and succession of black-odor waters (BOWs). In the field-scale investigation, livestock breeding wastewater (56.7 ± 3.2%) was the most critical microbial source. Moreover, fermentation (27.1 ± 4.4%) was found to be the dominant function. Combined with laboratory experiments, the critical environmental factors, such as total organic carbon (30–100 mg/L), ammonia nitrogen (2.5–9 mg/L), initial dissolved oxygen (2–8 mg/L) and chlorophyll a (0–90 mg/L), impacted the intensity of blackening. The differentiation of ecological niches within the microbial community played a significant role in driving the blackening speed. In laboratory-scale experiments, the microbial ecological niche determined the blackening timing and dominations of the stochastic processes in the microbial assembly process (88 - 51%). The three stages, including the anaerobic degradation stage, blackening stage and slow recovery stage, were proposed to understand the assembly of the microbial communities. These findings enhance our understanding of microorganisms in BOWs and provide valuable insights for detecting and managing heavily organic polluted waters.

Redox gradients drive microbial community assembly patterns and molecular ecological networks in the hyporheic zone of effluent-dominated rivers

The impacts of effluent discharge on receiving waterbodies have been a research hotspot. Nonetheless, limited information is available on the microbial community assembly patterns in the hyporheic zones (HZ) responding to the changes in the microenvironments, e.g., solute transport and redox gradient variations. Using two representative effluent-dominated rivers as model systems, the spatio-temporal bacterial community dynamics and assembly patterns in oxic and suboxic zones in the shallow riverbed sediments were disentangled via null model- and neutral model-based approaches. Bacterial dynamics in community composition were observed driven by environmental filtering, i.e., impacts of environmental variables, more than geographic distances, i.e., the depths of sediments. The communities in samples collected in summer were largely shaped by stochasticity, in which homogeneous selection occupied a higher proportion in oxic (∼39%) than in suboxic zone (∼23%). Deterministic processes contributed to a more complex community structure for samples from oxic zones, whereas weakened the interspecies interactions in suboxic zones. The richness and abundances of non-neutral community were confirmed governing the deterministic assembly in oxic zones. Key species ascribed to ‘connectors’ and ‘network hubs’ dominated the community assembly variations in samples collected in winter, and in oxic zones, respectively. Significant positive relationships between β-nearest taxon index and dissolved organic nitrogen (DON) and nitrate highlighted their vital roles in community assembly via deterministic selective pressures in oxic zones. The significance thresholds of nitrogen species for community transition in winter (ΔDON: 2.81 mg-N/L, ΔNO3−: 1.09 mg-N/L) were lower than in summer, probably implying that stricter effluent quality standards should be established in colder seasons. Combined, our work poses first insights on the roles of redox zonation in driving microbial community assembly in HZ, which is of significance in guiding ecological remediation processes in effluent-dominated rivers.

Mechanisms and responses of nitrogen transformations mediated by microbial communities in constructed tailwater wetlands to salinity stress

The long-term salinity stress may affect the nitrogen transformation processes and microbial community assembly patterns in constructed wetlands treating tailwater, influencing their operational effectiveness. In this study, we employ 16S rRNA gene sequencing, combined with multivariate ecological and statistical methods, to investigate interactions between bacterial community diversity and nitrogen transformation genes in constructed tailwater wetlands under salinity stress. The results revealed that long-term salinity stress led to reduced microbial diversity and increased community heterogeneity. Additionally, salinity stress led to decreased functionality of microbial community, intensified competition, and elevated expression of functional genes. Furthermore, as predicted by PICRUSt2, long-term salinity stress resulted in overall inhibition of community nitrogen conversion functions, while short-cut nitrification-denitrification processes played a bigger part in nitrogen conversion. Moreover, the symbiotic nitrogen fixation process was promoted, while the competing dissimilatory nitrate reduction process was inhibited. Salinity can greatly explain the apparent differences in microbial communities and nitrogen transformation potential in saline constructed wetland systems compared to common wetlands. These findings provide novel insights into the mechanisms underlying nitrogen transformation processes in constructed tailwater wetlands under long-term salinity stress and important implications for redesign and renovations of constructed wetlands.

Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome.

Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain unclear, with previous studies reporting contradictory results regarding the importance of bacterial dispersal versus host selection. This discrepancy could be driven in part because leaf microbiome studies typically consider the upper and lower leaf surfaces as a single entity despite these habitats possessing considerable anatomical differences. We characterized the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces across 24 plant species. Leaf surface pH and stomatal density were found to shape phyllosphere community composition, and the underside of leaves had lower richness and higher abundances of core community members than upper leaf surfaces. We found fewer endemic bacteria on the upper leaf surfaces, suggesting that dispersal is more important in shaping these communities, with host selection being a more important force in microbiome assembly on lower leaf surfaces. Our study illustrates how changing the scale in which we observe microbial communities can impact our ability to resolve and predict microbial community assembly patterns on leaf surfaces. IMPORTANCE Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves.

A comparison of microbial composition under three tree ecosystems using the stochastic process and network complexity approaches.

Soil microbes act as “players” in regulating biogeochemical cycles, whereas environmental heterogeneity drives microbial community assembly patterns and is influenced by stochastic and deterministic ecological processes. Currently, the limited understanding of soil microbial community assembly patterns and interactions under temperate forest stand differences pose a challenge in studying the soil microbial involvement during the succession from coniferous to broad-leaved forests. This study investigated the changes in soil bacterial and fungal community diversity and community structure at the regional scale and identified the pathways influencing soil microbial assembly patterns and their interactions. The results showed that broad-leaved forest cover in temperate forests significantly increased soil pH, and effectively increased soil water content, total carbon (TC), total nitrogen (TN), and total phosphorus (TP) contents. Both soil bacterial and fungal alpha diversity indices were correlated with soil physicochemical properties, especially in broad-leaved forest. The bacterial and fungal community composition of coniferous forest was dominated by deterministic process (bacteria: 69.4%; fungi: 88.9%), while the bacterial community composition of broad-leaved forest was dominated by stochastic process (77.8%) and the fungal community composition was dominated by deterministic process (52.8%). Proteobacteria, Acidobacteriota, Actinobacteriota, and Verrucomicrobiota were the dominant phyla of soil bacterial communities in temperate forests. Whereas Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota were the dominant phyla of soil fungal communities in temperate forests. Most members of dominant phylum were regulated by soil physical and chemical properties. In addition, the succession from temperate coniferous forest to broad-leaved forest was conducive to maintaining the complex network of soil bacteria and fungi, and the top 20 degree of the major taxa in the network reflected the positive response of microbial interactions to the changes of soil nutrients during forest succession. This study not only shows the mechanism by which species differences in temperate forests of northern China affect soil microbial community assembly processes, but also further emphasizes the importance of the soil microbiome as a key ecosystem factor through co-occurrence network analysis.

Application of thifluzamide alters microbial network structure and affects methane cycle genes in rice-paddy soil.

Thifluzamide is an effective agent for controlling rice sheath blight and has a long half-life in soil. However, the effects of thifluzamide on the abundance of microbes harboring methane-cycle genes and soil microbial community assembly patterns are not well known. Thus, we conducted a three-month indoor mesocosm experiment to ascertain the effects of thifluzamide (0.05, 0.5, and 5 mg kg-1 soil; 0.05 mg kg-1 soil being recommended) on bacterial and archaeal community structure and on the abundance of methanogen genes using two typical paddy soils: sandy soil from Hangzhou (HZ) and loam sandy soil from Jiansanjiang (JSJ). The effects of thifluzamide on soil microorganisms were related to soil type. In JSJ loam sandy soil, thifluzamide significantly increased bacterial α diversity after 7-30 d and archaeal α diversity at 30 and 60 d. In HZ sandy soil, however, α diversity did not change significantly. Network analysis showed that thifluzamide-treated soils possessed more complex networks with more total nodes and links, a higher average degree of connectivity, and more keystone species. Thifluzamide application increased the number of keystone species associated with methane production in both types of paddy soil. A relatively greater number of modules were significantly negatively correlated with mcrA abundance in the HZ T10 network, but more modules were positively correlated with mcrA abundance in the JSJ T100 network. The half-life of thifluzamide varied for the different doses, i.e., from 152.0 to 419.6 d. The results reveal that methane-cycle genes, soil microbiome assembly, and interactions among microbial species all change in response to thifluzamide stress.

Assembly Patterns of the Rhizosphere Microbiome Along the Longitudinal Root Axis of Maize (Zea mays L.).

It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil – their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize (Zea mays L.). We grew maize plants in an agricultural loamy soil and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of operational taxonomic unit (OTU) richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Further up the root where lateral roots emerged processes of community assembly appeared to be more deterministic (e.g., through competition and predation). This shift toward significance of deterministic processes was revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Such patterns were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is crucially important.

Stochasticity versus determinism: Microbial community assembly patterns under specific conditions in petrochemical activated sludge

The pattern of microbial community assembly in petrochemical sludge is not well-explained. In this study, three kinds of petrochemical activated sludge (AS) from the same seed sludge were investigated to determine their microbial assembly pattern for long-term adaptation. Beta Nearest Taxon Index analysis revealed that the assembly strategies of the abundant and rare operational taxonomic unit (OTU) sub-communities are different for archaeal and bacterial communities. Abundant OTUs preferred deterministic processes, whereas rare OTUs randomly formed due to weak selection. Canonical correspondence analysis/variation partition analysis and Mantel testing results revealed that ammonium, petroleum, and chromium (Cr (VI)) mainly structured the abundant sub-communities. On the other hand, environmental variables, including ammonium, petroleum, and heavy metals, shaped the rare sub-communities. The PICRUSt2 tool was used to predict the functions. Results indicated a greater abundance of microbes harboring the hydrocarbon degradation pathway and heavy-metal-resistant enzymes. Cross-treatment experiments using one type of AS to treat the other two kinds of wastewater were conducted. The results of the cross-treatment experiments and qPCR both suggest the functional adaptation of the microbial community. We revealed selection strategies for the adaptation of bacteria and archaea in AS during environmental changes, providing a theoretical basis for petrochemical wastewater treatment.

Phylogenetic Responses of Marine Free-Living Bacterial Community to Phaeocystis globosa Bloom in Beibu Gulf, China.

Phaeocystis globosa blooms are recognized as playing an essential role in shaping the structure of the marine community and its functions in marine ecosystems. In this study, we observed variation in the alpha diversity and composition of marine free-living bacteria during P. globosa blooms and identified key microbial community assembly patterns during the blooms. The results showed that the Shannon index was higher before the blooming of P. globosa in the subtropical bay. Marinobacterium (γ-proteobacteria), Erythrobacter (α-proteobacteria), and Persicobacter (Cytophagales) were defined as the most important genera, and they were more correlated with environmental factors at the terminal stage of P. globosa blooms. Furthermore, different community assembly processes were observed. Both the mean nearest relatedness index (NRI) and nearest taxon index (NTI) revealed the dominance of deterministic factors in the non-blooming and blooming periods of P. globosa, while the bacterial communities in marine waters after the blooms tended to be controlled by stochastic factors. Our findings revealed that the assembly of the bacterial community in marine P. globosa blooms is a complex process with mixture effects of marine microbiomes and environmental parameters.

Microbial niches in raw ingredients determine microbial community assembly during kimchi fermentation

Fermented foods constitute hubs of microbial consortia differentially affecting nutritional and organoleptic properties, quality, and safety. Here we show the origin source of fermentative microbes and fermentation dynamics of kimchi. We partitioned microbiota by raw ingredient (kimchi cabbage, garlic, ginger, and red pepper) to render kimchi fermented by each source-originated microbe pool and applied multi-omics (metataxonomics and metabolomics), bacterial viability, and physiochemical analyses to longitudinally collected samples. Only kimchi cabbage- and garlic-derived microbial inoculums yielded successful kimchi fermentations. The dominant fermentative microbial taxa and subsequent metabolic outputs differed by raw ingredient type: the genus Leuconostoc, Weissella, and Lactobacillus for all non-sterilized ingredients, garlic, and kimchi cabbage, respectively. Gnotobiotic kimchi inoculated by mono-, di-, and tri- isolated fermentative microbe combinations further revealed W. koreensis-mediated reversible microbial metabolic outputs. The results suggest that the raw ingredient microbial habitat niches selectively affect microbial community assembly patterns and processes during kimchi fermentation.

Dominant Tree Species Shape Soil Microbial Community via Regulating Assembly Processes in Planted Subtropical Forests

Understanding the ecological processes that regulate microbial community assembly in different habitats is critical to predict microbial responses to anthropogenic disturbances and environmental changes. Rubber (Hevea brasiliensis) and Eucalypt (Eucalyptus urophylla) plantations (thereafter RP and EP) are rapidly established at the expense of forests in tropical China, greatly affecting tropical soils and their processes. However, the assembly processes of soil microbial communities after forest conversions remain unclear. We investigated soil microbial communities’ attributes and quantified the portion of deterministic assembly variation in two RP (a 3- and a 5-year-old) and two EP (a 2- and a 4-year-old) in Southern China. Shannon and Faith’s Phylogenetic α-diversity of both bacterial and fungal communities were higher in RP than in EP, regardless of plantation age or soil depth (0–50 cm). Bacterial and fungal community structure was significantly different among the four plantations. The dominant microbial taxa in RP closely tracked the availability of nitrogen, phosphorus and potassium (K) while those in EP were closely related to the high total K content. Microbial co-occurrence networks in RP were more modular than those in EP, as governed by more keystone taxa that were strongly dependent on soil available nutrients. Environmental filtering imposed by soil nutrients heterogeneity contributed a considerable portion (33–47%) of bacterial assembly variation in RP, but much less (8–14%) in EP. The relative contribution of environmental selection on fungal assembly was also greater in RP than in EP. Our findings suggest that in RP clear microbial community patterns exist with respect to soil nutrients, whereas in EP microbial community assembly patterns are more stochastic and variable. The large variation in soil microbial community assembly patterns in EP could lead to fragile and unstable microbial-soil relationships, which may be one factor driving soil degradation in EP.

Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly.

Flavonoids are a group of polyphenolic dietary compounds found in many different plant-based foods. There is increasing evidence that higher flavonoid intake may be causally linked to a reduced risk of cardiovascular disease and other chronic diseases. The bioactivity and bioavailability of many dietary flavonoids can be influenced by gastrointestinal microbiome metabolism. However, the role that habitual flavonoid intake plays in shaping the human gut microbiome is poorly understood. We describe an application of an ecosystem-based analytic approach to nutritional, microbiome, and questionnaire data from a cohort of more than 240 generally healthy adult males to assess the role of dietary flavonoid compounds in driving patterns of microbial community assembly. We identified six subclass-specific microbial communities (SMCs) uniquely and independently associated with intakes of the six flavonoid subclasses. Eggerthela lenta was positively associated with intakes of flavonol and flavanone, and Adlercreutzia equolifaciens was positively associated with intakes of flavonols and flavanol monomers. In contrast, for nearly all flavonoid subclasses, Flavonifractor plautii was inversely associated with subclass consumption. Consuming tea at least once per week explained 10.4% of the total variance in assembly of the 20 species comprising the flavanol monomer SMC. The novel methodology employed, necessitated by multidimensional microbiome data that consist of nonindependent features that exhibit a wide range of distributions and mean values, addresses a major challenge in our ability to understand associations of the microbiome in a wide range of clinical and epidemiologic settings.IMPORTANCE Dietary flavonoids, which have been implicated in lowering chronic disease risk and improving blood pressure, represent a diverse group of polyphenolic compounds found in many commonly consumed foods such as tea, red wine, apples, and berries. The bioactivity and bioavailability of more dietary flavonoids can be influenced by gastrointestinal microbiome metabolism. With demonstrated prebiotic and antimicrobial effects in in vitro and in animal models, it is surprising that there are not many human studies investigating the role dietary flavonoids play in shaping the gastrointestinal microbiome. Our analysis revealed patterns of community assembly that uniquely and independently characterize an individual's exposure to various flavonoid compounds. Furthermore, this study confirmed, independent from effects of other dietary and lifestyle factors included in the multivariate-adjusted model, that flavonoid intake is associated with microbial community assembly.

Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes.

Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms.IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.

Drivers and patterns of microbial community assembly in a Lyme disease vector.

Vector‐borne diseases constitute a major global health burden and are increasing in geographic range and prevalence. Mounting evidence has demonstrated that the vector microbiome can impact pathogen dynamics, making the microbiome a focal point in vector‐borne disease ecology. However, efforts to generalize preliminary findings across studies and systems and translate these findings into disease control strategies are hindered by a lack of fundamental understanding of the processes shaping the vector microbiome and the interactions therein. Here, we use 16S rRNA sequencing and apply a community ecology framework to analyze microbiome community assembly and interactions in Ixodes pacificus, the Lyme disease vector in the western United States. We find that vertical transmission routes drive population‐level patterns in I. pacificus microbial diversity and composition, but that microbial function and overall abundance do not vary over time or between clutches. Further, we find that the I. pacificus microbiome is not strongly structured based on competition but assembles nonrandomly, potentially due to vector‐specific filtering processes which largely eliminate all but the dominant endosymbiont, Rickettsia. At the scale of the individual I. pacificus, we find support for a highly limited internal microbial community, and hypothesize that the tick endosymbiont may be the most important component of the vector microbiome in influencing pathogen dynamics.

Assessing Microbial Community Patterns During Incipient Soil Formation From Basalt

AbstractMicrobial dynamics drive the biotic machinery of early soil evolution. However, integrated knowledge of microbial community establishment, functional associations, and community assembly processes in incipient soil is lacking. This study presents a novel approach of combining microbial phylogenetic profiling, functional predictions, and community assembly processes to analyze drivers of microbial community establishment in an emerging soil system. Rigorous submeter sampling of a basalt‐soil lysimeter after 2 years of irrigation revealed that microbial community colonization patterns and associated soil parameters were depth dependent. Phylogenetic analysis of 16S rRNA gene sequences indicated the presence of diverse bacterial and archaeal phyla, with high relative abundance of Actinomyceles on the surface and a consistently high abundance of Proteobacteria (Alpha, Beta, Gamma, and Delta) at all depths. Despite depth‐dependent variation in community diversity, predicted functional gene analysis suggested that microbial metabolisms did not differ with depth, thereby suggesting redundancy in functional potential throughout the system. Null modeling revealed that microbial community assembly patterns were predominantly governed by variable selection. The relative influence of variable selection decreased with depth, indicating unique and relatively harsh environmental conditions near the surface and more benign conditions with depth. Additionally, community composition near the center of the domain was influenced by high levels of dispersal, suggesting that spatial processes interact with deterministic selection imposed by the environment. These results suggest that for oligotrophic systems, there are major differences in the length scales of variation between vertical and horizontal dimensions with the vertical dimension dominating variation in physical, chemical, and biological features.

Application of the microbial community coalescence concept to riverine networks.

Flows of water, soil, litter, and anthropogenic materials in and around rivers lead to the mixing of their resident microbial communities and subsequently to a resultant community distinct from its precursors. Consideration of these events through a new conceptual lens, namely, community coalescence, could provide a means of integrating physical, environmental, and ecological mechanisms to predict microbial community assembly patterns better in these habitats. Here, we review field studies of microbial communities in riverine habitats where environmental mixing regularly occurs, interpret some of these studies within the community coalescence framework and posit novel hypotheses and insights that may be gained in riverine microbial ecology through the application of this concept. Particularly in the face of a changing climate and rivers under increasing anthropogenic pressures, knowledge about the factors governing microbial community assembly is essential to forecast and/or respond to changes in ecosystem function. Additionally, there is the potential for microbial ecology studies in rivers to become a driver of theory development: riverine systems are ideal for coalescence studies because regular and predictable environmental mixing occurs. Data appropriate for testing community coalescence theory could be collected with minimal alteration to existing study designs.

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly.

Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant-microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem. Here, using a combination of comparative genomics and exometabolomics, we show that pre-programmed developmental processes in plants (Avena barbata) result in consistent patterns in the chemical composition of root exudates. This chemical succession in the rhizosphere interacts with microbial metabolite substrate preferences that are predictable from genome sequences. Specifically, we observed a preference by rhizosphere bacteria for consumption of aromatic organic acids exuded by plants (nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic). The combination of these plant exudation traits and microbial substrate uptake traits interact to yield the patterns of microbial community assembly observed in the rhizosphere of an annual grass. This discovery provides a mechanistic underpinning for the process of rhizosphere microbial community assembly and provides an attractive direction for the manipulation of the rhizosphere microbiome for beneficial outcomes.

Microbial diversity in an intensively managed landscape is structured by landscape connectivity

Intensively managed land increases the rate of nutrient and particle transport within a basin, but the impact of these changes on microbial community assembly patterns at the basin scale is not yet understood. The objective of this study was to investigate how landscape connectivity and dispersal impacts microbial diversity in an agricultural-dominated watershed. We characterized soil, sediment and water microbial communities along the Upper Sangamon River basin in Illinois-a 3600 km2 watershed strongly influenced by human activity, especially landscape modification and extensive fertilization for agriculture. We employed statistical and network analyses to reveal the microbial community structure and interactions in the critical zone (water, soil and sediment media). Using a Bayesian source tracking approach, we predicted microbial community connectivity within and between the environments. We identified strong connectivity within environments (up to 85.4±13.3% of sequences in downstream water samples sourced from upstream samples, and 44.7±26.6% in soil and sediment samples), but negligible connectivity across environments, which indicates that microbial dispersal was successful within but not between environments. Species sorting based on sample media type and environmental parameters was the dominant driver of community dissimilarity. Finally, we constructed operational taxonomic unit association networks for each environment and identified a number of co-occurrence relationships that were shared between habitats, suggesting that these are likely to be ecologically significant.

Decreases in average bacterial community rRNA operon copy number during succession.

Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.

Landscape position influences microbial composition and function via redistribution of soil water across a watershed.

Subalpine forest ecosystems influence global carbon cycling. However, little is known about the compositions of their soil microbial communities and how these may vary with soil environmental conditions. The goal of this study was to characterize the soil microbial communities in a subalpine forest watershed in central Montana (Stringer Creek Watershed within the Tenderfoot Creek Experimental Forest) and to investigate their relationships with environmental conditions and soil carbonaceous gases. As assessed by tagged Illumina sequencing of the 16S rRNA gene, community composition and structure differed significantly among three landscape positions: high upland zones (HUZ), low upland zones (LUZ), and riparian zones (RZ). Soil depth effects on phylogenetic diversity and β-diversity varied across landscape positions, being more evident in RZ than in HUZ. Mantel tests revealed significant correlations between microbial community assembly patterns and the soil environmental factors tested (water content, temperature, oxygen, and pH) and soil carbonaceous gases (carbon dioxide concentration and efflux and methane concentration). With one exception, methanogens were detected only in RZ soils. In contrast, methanotrophs were detected in all three landscape positions. Type I methanotrophs dominated RZ soils, while type II methanotrophs dominated LUZ and HUZ soils. The relative abundances of methanotroph populations correlated positively with soil water content (R = 0.72, P < 0.001) and negatively with soil oxygen (R = -0.53, P = 0.008). Our results suggest the coherence of soil microbial communities within and differences in communities between landscape positions in a subalpine forested watershed that reflect historical and contemporary environmental conditions.