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Soil bacterial communities play fundamental roles in ecosystem functioning and often display a skewed distribution of abundant and rare taxa. So far, relatively little is known about the biogeographical patterns and mechanisms structuring the assembly of abundant and rare biospheres of soil bacterial communities. Here, we studied the geographical distribution of different bacterial sub‐communities by examining the relative influence of environmental selection and dispersal limitation on taxa distributions in paddy soils across East Asia. Our results indicated that the geographical patterns of four different bacterial sub‐communities consistently displayed significant distance–decay relationships (DDRs). In addition, we found niche breadth and dispersal rates to significantly explain differences in community assembly of abundant and rare taxa, directly affecting the strength of DDRs. While conditionally rare and abundant taxa displayed the strongest DDR due to higher environmental filtering and dispersal limitation, moderate taxa sub‐communities had the weakest DDR due to greater environmental tolerance and dispersal rate. Random forest models indicated that soil pH (9.13%–49.78%) and average annual air temperature (16.59%–46.49%) were the most important predictors of the variation in the bacterial community. This study advances our understanding of the intrinsic links between fundamental ecological processes and microbial biogeographical patterns in paddy soils. [ABSTRACT FROM AUTHOR]

Sorghum is a major staple crop in sub-Saharan Africa with yields severely impacted by biotic and abiotic factors. Here, we analysed the taxonomic diversity and biogeographical distribution of bacterial taxa of 48 agricultural fields along a transect of approximately 2000 km across the Ethiopian sorghum belt, the centre of origin of sorghum. The ultimate goal is to identify—yet-unexplored—beneficial plant–microbe associations. Based on bulk soil bacterial communities and DArT-SNP analyses of 59 sorghum accessions, we selected three microbiologically distinct field soils and 12 sorghum genotypes, including commercial varieties, wild relatives, and farmer-preferred landraces. The results showed a core rhizosphere microbiome of 2125 amplicon sequence variants (ASVs), belonging to eight bacterial families consistently found across the three soil types and the 12 sorghum genotypes. Integration of the rhizosphere bacterial community analysis with DArT-SNP sorghum genotyping revealed the association of differentially abundant ASVs with sorghum genotypic traits, including the distinct recruitment of Pseudomonadaceae by the stay-green, drought-tolerant, and wild sorghum genotypes. Collectively, these results provide new insights into the core and accessory bacterial taxa in the sorghum rhizosphere in the centre of origin, setting a baseline for targeted isolation and functional characterization of putative beneficial rhizobacteria. [ABSTRACT FROM AUTHOR]

Beneficial host-associated bacteria can assist plant protection against pathogens. In particular, specific microbes are able to induce plant systemic resistance. However, it remains largely elusive which specific microbial taxa and functions trigger plant immune responses associated with disease suppression. Here, we experimentally studied this by setting up two independent microcosm experiments that differed in the time at which plants were exposed to the pathogen and the soil legacy (i.e., soils with historically suppressive or conducive). Overall, we found soil legacy effects to have a major influence on disease suppression irrespective of the time prior to pathogen exposure. Rhizosphere bacterial communities of tomato plants were significantly different between the two soils, with potential beneficial strains occurring at higher relative abundances in the suppressive soil. Root transcriptome analysis revealed the soil legacy to induce differences in gene expression, most importantly, genes involved in the pathway of phenylpropanoid biosynthesis. Last, we found genes in the phenylpropanoid biosynthesis pathway to correlate with specific microbial taxa, including Gp6, Actinomarinicola, Niastella, Phaeodactylibacter, Longimicrobium, Bythopirellula, Brevundimonas, Ferruginivarius, Kushneria, Methylomarinovum, Pseudolabrys, Sphingobium, Sphingomonas, and Alterococcus. Taken together, our study points to the potential regulation of plant systemic resistance by specific microbial taxa, and the importance of soil legacy on disease incidence and eliciting plant-defense mechanisms. [ABSTRACT FROM AUTHOR]

Summary: The mechanisms underlying microbial community dynamics and co‐occurrence patterns along ecological succession are crucial for understanding ecosystem recovery but remain largely unexplored. Here, we investigated community dynamics and taxa co‐occurrence patterns in bacterial and fungal communities across a well‐established chronosequence of post‐mining lands spanning 54 years of recovery. Bacterial community structures became increasingly phylogenetically clustered with soil age at early successional stages and varied less at later successional stages. The dynamics of bacterial community phylogenetic structures were determined by the changes in the soil vegetation cover along succession. The dynamics of fungal community phylogenetic structures did not significantly correlate with soil age, soil properties or vegetation cover, and were mainly attributed to stochastic processes. Along succession, the common decrease in the bacterial co‐occurrence complexity and in the average pairwise phylogenetic distances between co‐occurring bacteria implied a decrease in potential bacterial cooperation. The increased complexity of fungal co‐occurrence along succession was independent of phylogenetic relatedness between co‐occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession. [ABSTRACT FROM AUTHOR]

Understanding how species interaction and assembly processes structure the abundant and rare bacterial biosphere in soils is crucial for predicting how biodiversity influences ecosystem functioning. Here, we profiled the bacterial communities across a salt marsh ecosystem gradient to investigate the co-occurrence patterns across taxa and the relative influence of ecological processes mediating the assembly of the abundant and rare biospheres in soil. Our results revealed abundant taxa to be ubiquitous across all sample sites, whereas the distributions of the rare taxa were relatively more site-specific. The alpha-diversity indices and beta-diversity of rare sub-communities were significantly higher than those of the abundant sub-communities. Besides, both the taxonomic and functional composition of soil bacterial communities significantly differed between the two biospheres. Furthermore, the influence of stochasticity differed in each sub-community. In particular, stochastic processes were relatively more important in constraining the rare taxa assembly. Co-occurrence network analysis revealed that a few abundant taxa occupy central nodes within the networks, possibly indicating crucial roles as keystone taxa. Collectively, these findings suggest that abundant and rare bacterial biospheres have distinct distributions underpinned by a dynamic interplay of ecological processes and taxa co-occurrence patterns. [ABSTRACT FROM AUTHOR]

In Drosophila, diet is considered a prominent factor shaping the associated bacterial community. However, the host population background (e.g. genotype, geographical origin and founder effects) is a factor that may also exert a significant influence and is often overlooked. To test for population background effects, we characterized the bacterial communities in larvae of six genetically differentiated and geographically distant D. melanogaster lines collected from natural populations across Europe. The diet for these six lines had been identical for ca. 50 generations, thus any differences in the composition of the microbiome originates from the host populations. We also investigated whether induced shifts in the microbiome—in this case by controlled antibiotic administration—alters the hosts’ resistance to parasitism. Our data revealed a clear signature of population background on the diversity and composition of D. melanogaster microbiome that differed across lines, even after hosts had been maintained at the same diet and laboratory conditions for over 4 years. In particular, the number of bacterial OTUs per line ranged from 8 to 39 OTUs. Each line harboured 2 to 28 unique OTUs, and OTUs that were highly abundant in some lines were entirely missing in others. Moreover, we found that the response to antibiotic treatment differed among the lines and significantly altered the host resistance to the parasitoid Asobara tabida in one of the six lines. Wolbachia, a widespread intracellular endosymbiont associated with parasitoid resistance, was lacking in this line, suggesting that other components of the Drosophila microbiome caused a change in host resistance. Collectively, our results revealed that lines that originate from different population backgrounds show significant differences in the established Drosophila microbiome, outpacing the long-term effect of diet. Perturbations on these naturally assembled microbiomes to some degree influenced the hosts’ resistance against natural parasites. [ABSTRACT FROM AUTHOR]

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. [ABSTRACT FROM AUTHOR]

Ecological interactions are important for maintaining biodiversity and ecosystem functions. Particularly in stream biofilms, little is known about the distributional patterns of different taxonomic groups and their potential interactions along elevational gradients. Here, we investigated the bacterial and fungal community structures of stream biofilms across elevational gradients on Mount Kilimanjaro, and explored patterns of their distribution, diversity, community structures, and taxa co-occurrence. We found that fungal and bacterial richness were more convergent at higher elevations, while their community structures became significantly more divergent. Inferred network complexity and stability significantly decreased with increasing elevation for fungi, while an opposite trend was observed for bacteria. Further quantitative analyses showed that network structures of bacteria and fungi were more divergent as elevation increased. This pattern was strongly associated with shifts in abiotic factors, such as mean annual temperatures, water PO 4 3--P, and stream width. By constructing bipartite networks, we showed the fungal-bacterial network to be less redundant, more clustering, and unstable with increasing elevation. Abiotic factors (e.g., temperatures and stream width) and microbial community properties (i.e., structure and composition) significantly explained the dynamic changes in fungal-bacterial network properties. Taken together, this study provides evidence for the interplay of biotic and abiotic factors structuring potential microbial interactions in stream biofilms along a mountainside elevational gradient. • Differences in richness and structure of bacteria and fungi covaried with elevation. • Network complexity and stability were significantly higher for bacteria than fungi. • Network properties of bacteria and fungi were more divergent at higher elevations. • The stability of fungal-bacterial network strongly decreased at lower temperatures. • Biotic and abiotic factors significantly explain patterns in microbial co-occurrence. [ABSTRACT FROM AUTHOR]

Quantifying which assembly processes structure microbiomes can assist prediction, manipulation, and engineering of community outcomes. However, the relative importance of these processes might depend on whether DNA or RNA are used, as they differ in stability. We hypothesized that RNA-inferred community responses to (a)biotic fluctuations are faster than those inferred by DNA; the relative influence of variable selection is stronger in RNA-inferred communities (environmental factors are spatiotemporally heterogeneous), whereas homogeneous selection largely influences DNA-inferred communities (environmental filters are constant). To test these hypotheses, we characterized soil bacterial communities by sequencing both 16S rRNA amplicons from the extracted DNA and RNA transcripts across distinct stages of soil primary succession and quantified the relative influence of each assembly process using ecological null model analysis. Our results revealed that variations in α-diversity and temporal turnover were higher in RNA- than in DNA-inferred communities across successional stages, albeit there was a similar community composition; in line with our hypotheses, the assembly of RNA-inferred community was more closely associated with environmental variability (variable selection) than using the standard DNA-based approach, which was largely influenced by homogeneous selection. This study illustrates the need for benchmarking approaches to properly elucidate how community assembly processes structure microbial communities. [ABSTRACT FROM AUTHOR]

Bacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly are poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high-marsh, using the 16S rRNA gene amplicon sequencing. Bacterial community composition differed significantly between sediment transects. Physico-chemical properties, particularly sediment nutrient levels [i.e., total nitrogen (TN) and available phosphorus (AP)], as well as sediment physical structure and pH (P < 0.05) were strongly associated with the overall community variations. In addition, the topological properties of bacterial co-occurrence networks varied with the distance to the water-land junction. Both node- and network-level topological features revealed the bacterial network of sediments farthest from the junction to be less intense in complexity and interactions compared with other sediments. Phylogenetic null modelling analysis showed a progressive transition from stochastic to deterministic community assembly for the water-land junction sites toward the emerging terrestrial system. Taken together, this study provides a detailed outline of the distribution pattern of sediment bacterial community across the estuarine marsh and inform on the mechanisms and processes mediating bacterial community assembly in marsh soils. [ABSTRACT FROM AUTHOR]

Understanding how distinct processes operate in mediating community assembly is a long-standing theme in (microbial) ecology. Particularly in soil microbial communities, we still lack a fundamental appreciation of how assembly processes structure communities at the fine-scale level of soil aggregates. In this study, samples from a long-term agricultural field subjected to different fertilization regimes were used to quantify the relative influences of stochastic and deterministic processes on soil bacterial community assembly. First, we found bacterial communities to be more phylogenetically clustered in larger soil aggregates comparatively to small aggregates (Spearman's r = −0.366, P < 0.05). Second, we found the overall relative influence of selection to gradually decrease with an increase of aggregate size (Mantel r = 0.161, P < 0.01). By partitioning aggregate sizes and fertilization regimes, we found that sites subjected to fertilization (including chemical, organic, and bio-organic fertilizers) displayed a stronger relaxation of selection and an increased influence of stochasticity with an increase in aggregate size; a pattern not significantly observed at the control (unfertilized) treatment. Collectively, our results highlight the importance of evaluating community assembly at the fine-scale levels of soil aggregates and illustrate how regional level disturbances (i.e., agricultural management) exert an influence on the dynamic interplay of stochastic and deterministic processes. • Bacterial communities are more phylogenetically clustered in larger soil aggregates. • Soil aggregates mediate the balance between stochastic and deterministic processes. • Deterministic process of homogeneous selection is dominated in all soil aggregates. [ABSTRACT FROM AUTHOR]