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Root-associated microbial communities have been widely studied in the model plant Arabidopsis thaliana, but have been much less explored in agronomically important crops. Here, we used deep pyrosequencing of bacterial 16S rRNA to identify and characterize the root-associated microbial community of three traditional rice cultivars (representing indica and japonica subspecies and a hybrid) cultivated in typical paddy soils from China. We separated the root microbiota into endosphere and rhizosphere compartments, which were found to be the major determinant of variation in the total root microbial community. The microbial communities in each rhizocompartment were strongly influenced by soil type, while rice genotype exhibited a small but significant influence on both endosphere and rhizosphere microbiota. Pairwise comparisons showed that the endophytic bacterial community of indica rice differed significantly from that of japonica rice, while no remarkable differences were noted when comparing the community of indica vs. hybrid or japonica vs. hybrid. A core functional rice endophytic microbiota was identified, which accounted for relative abundances of up to 72.5% of the total microbial community. The 88 core root operational taxonomic units (OTUs) mainly belonged to the phylum Proteobacteria specifically Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria. These results clarify the rice root-associated microbial community assemblage and facilitate the construction of an artificial core root microbiota to promote plant growth and resistance.

Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes.

Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, α-Proteobacteria, and the β-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates (r2 = 0.26, P < 0.001), while the abundances of β-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates (r2 = 0.35, P < 0.001 and r2 = 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria (r2 = 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and β-Proteobacteria (r2 = 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere soils. Together our survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals. By applying the copiotroph—oligotroph concept to soil microorganisms we can make specific predictions about the ecological attributes of various bacterial taxa and better understand the structure and function of soil bacterial communities.

Aims The present study was planned to investigate the diversity of 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing bacteria from the rhizosphere of wheat plants and subsequent evaluation of selected PGPR on growth enhancement of wheat seedlings under drought and saline conditions. Methods ACC deaminase producing plant growth promoting rhizobacteria (PGPR) were isolated from the rhizosphere of wheat and identified using 16S rRNA gene sequence analysis. Isolates were evaluated for various direct and indirect plant growth promoting (PGP) traits. Plant inoculation experiment was conducted using isolates IG 19 and IG 22 in wheat to assess their plant growth promotion potential under salinity and drought stress. Results Thirty-eight ACC deaminase producing PGPR were isolated which belonged to 12 distinct genera and falling into four phyla γ-proteobacteria, β-proteobacteria, Flavobacteria and Firmicutes. Klebsiella sp. was the most abundant genera and followed by Enterobacter sp. The isolates exhibited ACC deaminase activities ranging from 0.106-0.980 μM α-ketobutyrate μg protein⁻¹ h⁻¹. The isolates showed multiple PGP traits such as IAA production, phosphate, zinc, potassium solubilization and siderophore production. Enterobacter cloacae (IG 19) and Citrobacter sp. (IG 22) inoculated wheat seedlings showed notable increases in fresh and dry biomass under non-stress as well as under stressed condition. Conclusion To the best of our knowledge this is the first report of presence of ACC deaminase activity and other PGP traits from the genus Citrobacter and Empedobacter. Our finding revealed that the γ-proteobacteria group dominated the wheat rhizosphere. Plant inoculation with PGPR could be a sustainable approach to alleviate abiotic stresses in wheat plants. These native PGPR isolates could be used as potential biofertilizers for sustainable agriculture.

Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as “glue” for soil particles. However, little is known about the dynamics of “soil glue” producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential “soil glue” producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.

Background and aims In semiarid ecosystems, changes in plant communities are promoted under shrub canopies during restoration, but the link between shrub community restoration dynamics and changes in soil microbe communities is still unclear.MethodsWe characterized the community structure and plant interactions of soil microbes by combining different methodological approaches (including high-throughput sequencing of the 16S rRNA gene and ITS gene, analysis of phospholipid fatty acids (PLFAs) and chloroform fumigation) and the key driving factors along a successional gradient of Sophora moorcroftiana shrub community in the middle reaches of the Yarlung Zangbo River.ResultsSoil microbial biomass carbon (MBC) and nitrogen (MBN), total PLFAs, and alpha diversity increased significantly as the successional stage advanced, and MBC and MBN were positively correlated with the carbon and nitrogen contents in the soil. Mantel test showed that successional stage-induced changes in soil microbial beta diversity were mainly associated with shrub coverage and soil physicochemical properties. The relative abundances of bacterial PLFAs, particularly those of gram-negative bacteria, such as Bacteroidetes, Alphaproteobacteria and Betaproteobacteria, significantly decreased with succession; the opposite was true for Acidobacteria, Planctomycetes, Gemmatimonadetes Deltaproteobacteria and Gammaproteobacteria. However, the proportion of fungi did not significantly differ among the four successional stages; the dominant phyla were Ascomycota and Basidiomycota. ConclusionWe suggest that shrubs directly shape soil microbial communities or indirectly affect such communities by altering soil substrates. Our findings advance the current understanding of sand-stabilizing plant–soil interactions during natural restoration and the reversal of desertification in stressful desert ecosystems.

To study the influence of straw incorporation with and without straw decomposer on bacterial community structure and biological traits, a 3-year field experiments, including four treatments: control without fertilizer (CK), chemical fertilizer (NPK), chemical fertilizer plus 7500 kg ha −1 straw incorporation (NPKS), and chemical fertilizer plus 7500 kg ha −1 straw incorporation and 300 kg ha −1 straw decomposer (NPKSD), were performed in a rice-wheat cropping system in Changshu (CS) and Jintan (JT) city, respectively. Soil samples were taken right after wheat (June) and rice (October) harvest in both sites, respectively. The NPKS and NPKSD treatments consistently increased crop yields, cellulase activity, and bacterial abundance in both sampling times and sites. Moreover, the NPKS and NPKSD treatments altered soil bacterial community structure, particularly in the wheat harvest soils in both sites, separating from the CK and NPK treatments. In the rice harvest soils, both NPKS and NPKSD treatments had no considerable impacts on bacterial communities in CS, whereas the NPKSD treatment significantly shaped bacterial communities compared to the other treatments in JT. These practices also significantly shifted the bacterial composition of unique operational taxonomic units (OTUs) rather than shared OTUs. The relative abundances of copiotrophic bacteria ( Proteobacteria , Betaproteobacteria , and Actinobacteria ) were positively correlated with soil total N, available N, and available P. Taken together, these results indicate that application of straw incorporation with and without straw decomposer could particularly stimulate the copiotrophic bacteria, enhance the soil biological activity, and thus, contribute to the soil productivity and sustainability in agro-ecosystems.

Background and aims Seeds are inhabited by diverse bacterial and fungal taxa whose colonization patterns are little understood. We hypothesized, however, that specific niches within seeds host microbes. Methods In this study, the putative presence of bacteria, inhabiting the seed endosphere of an angiosperm, the melon Cucumis melo reticulatus group cv. 'Dulce', was examined by scanning electron microscopy (SEM) and confocal laser-scanning microscopy coupled with double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH). Results SEM images showed microbial-like structures in different tissues and FISH revealed endophytic bacteria colonizing the outer and inner seed parts, on perisperm/endosperm envelope, inside the cotyledons as parts of the embryo, and, to a lesser extent, inside embryonic hypocotyl-root axis tissues. Alphaproteobacteria were shown to inhabit the seed coat and the envelope surrounding the embryonic hypocotyl-root tissues, but could not be seen in the cotyledons, whereas Betaproteobacteria were only detected in the outer seed coat. Some Gammaproteobacteria were also seen in the outer seed coat, but were mainly visualized in the cotyledons with a few inside the seed's embryonic hypocotyl-root tissues, among other bacteria. Firmicutes were visualized inside the seed coat, but mostly inside the cotyledon tissues, on the perisperm/endosperm envelope and inside the embryonic hypocotyl-root axis tissues. Microscopy revealed Actinobacteria inside the inner and outer seed coat and inside the embryonic parts such as cotyledons, with a few inside the hypocotyl-root axis. Conclusions This is the first demonstration of niches for the most active groups of bacteria inhabiting different seed tissues of an angiosperm.

In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. The gut digesta and egested fecal pellets exhibited a microbial profile comprised of Gammaproteobacteria, mainly Vibrio, and Bacteroidetes. Both the seagrass and surrounding sea water revealed Alpha- and Betaproteobacteria. Bray–Curtis distances of microbial communities indicated a clustering profile with low intrasample variation. Predictive metagenomics performed on the microbial communities revealed that the gut tissue had high relative abundances of metabolisms assigned to the KEGG-Level-2 designation of energy metabolisms compared to the gut digesta, which had higher carbohydrate, amino acid and lipid metabolisms. Overall, the results of this study elaborate the spatial distribution of microbial communities in the gut ecosystem of L. variegatus, and specifically a selective attribute for Campylobacteraceae in the gut tissue. Also, the predictive functional significance of bacterial communities in uniquely compartmentalized gut ecosystems of L. variegatus has been described. This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Graphical Abstract Figure. This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico.

Antibiotic ciprofloxacin is ubiquitous in the environment. However, little is known about ciprofloxacin dissipation by microbial community. The present study investigated the biodegradation potential of ciprofloxacin by mixed culture and the influential factors and depicted the structure of ciprofloxacin-degrading microbial community. Both the original microbiota from drinking water biofilter and the microbiota previously acclimated to high levels of ciprofloxacin could utilize ciprofloxacin as sole carbon and nitrogen sources, while the acclimated microbiota had a much stronger removal capacity. Temperature rise and the presence of carbon or nitrogen sources favored ciprofloxacin biodegradation. Many novel biotransformation products were identified, and four different metabolic pathways for ciprofloxacin were proposed. Bacterial community structure illustrated a profound shift with ciprofloxacin biodegradation. The ciprofloxacin-degrading bacterial community was mainly composed of classes Gammaproteobacteria , Bacteroidia , and Betaproteobacteria . Microorganisms from genera Pseudoxanthomonas , Stenotrophomonas , Phenylobacterium , and Leucobacter might have links with the dissipation of ciprofloxacin. This work can provide some new insights towards ciprofloxacin biodegradation.