Search

A field experiment was carried out to investigate the impact of two improved tillage systems (conventional tillage combined with the incorporation of solid anaerobic digestate, no-tillage) on the prokaryotic community composition in two tree orchard (olive, citrus) soils with contrasting texture, carbonate content, and pH, located in Southern Italy. Soil samples were taken over a 5-month period to assess immediate (2 days) vs short-term (7 and 18 weeks) responses. Phylogenetic diversity and compositional shifts of both total and metabolically active soil prokaryotic communities were assessed by next-generation sequencing of 16S rRNA gene templates from soil-extracted DNA/RNA. In both digestate-treated soils, copiotrophic α-Proteobacteria and oligotrophic Acidobacteria, Gemmatimonadetes, and Verrucomicrobia showed an immediate (2 days) but short-lived (7 weeks) shift in their relative abundance similar in persistence but not in magnitude; whereas selective soil type-dependent responses were observed for Actinobacteria, Chloroflexi, Firmicutes, and Planctomycetes. The autochthonous soil microbiota demonstrated resilience to the addition of the anaerobic digestate, which was dominated by Firmicutes, Bacteroidetes, Deinococcus-Thermus, and Euryarchaeota (Methanomicrobia). Likewise, a temporary increase in the relative abundances of copiotrophic taxa (Firmicutes, Bacteroidetes, Thaumarchaeota) was observed under conventional tillage, especially in the sandy loam (citrus) soil. Conversely, no-tillage favored the establishment of oligotrophic Chloroflexi and Verrucomicrobia in both soils. The active and the total prokaryotic communities differed from each other only in physically disturbed soils. Soil management induced compositional shifts in the predominant microbial copiotrophic/oligotrophic community balance, whose persistence was linked to the tillage system, while magnitude depended on soil type.

To improve our understanding of early microbial colonization of pristine minerals and their group-specific C utilization, we exposed minerals (illite/goethite/quartz) amended with artificial root exudates (ARE, glucose, and citric acid) in grassland soils for a period of 24 weeks. FTIR spectra indicated that mineral-associated ARE were used within the first 2 weeks of exposure and were replaced by other carbohydrates derived from living or dead cells as well as soil-borne C sources transported into the mineralosphere after heavy rain events. Fungi and Gram-positive bacteria incorporated ARE-derived C more rapidly than Gram-negative bacteria. Gram-negative bacteria presumably profited indirectly from the ARE by cross-feeding on mineral-associated necromass of fungi and Gram-positive bacteria. The Gram-negative bacterial phyla Verrucomicrobia, Planctomycetes, Gemmatimonadetes, Armatimonadetes, and Chloroflexi showed a positive correlation with Gram-negative PLFA abundances. After 24 weeks of exposure in the grassland soils, abundances of soil microorganisms in the mineralosphere reached only 3.1% of the population density in soil. In conclusion, both bacteria and fungi slowly colonize new surfaces such as pristine minerals, but quickly assimilate artificial root exudates, creating an active microbial community in the mineralosphere.

Plant roots and soil prokaryotes primarily interact with each other in the rhizosphere. Changes in the rhizosphere prokaryotic structure are influenced by several factors. In this study, the community structure of the Potentilla anserina L. rhizosphere prokaryotes was identified and evaluated by high-throughput sequencing technology in different continuous cropping fields and developmental stages of the plant. In total, 2 archaeal (Euryarchaeota and Thaumarchaeota) and 26 bacterial phyla were identified in the P. anserina rhizosphere. The bacterial community was mainly composed of Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria, and Verrucomicrobia. Moreover, the prokaryotic community structure of the rhizosphere varied significantly during plant development. Our results provide new insights into the dynamics of the P. anserina rhizosphere prokaryotic community and may provide useful information for enhancing the growth and development of P. anserina through artificial control of the soil prokaryotes.

Bacteria are divided primarily into monoderms (with one cell membrane, and usually Gram-positive, due to a thick peptidoglycan layer) and diderms (with two cell membranes, and mostly Gram-negative, due to a thin peptidoglycan layer sandwiched between the two membranes). Photosynthetic species are spread among the taxonomic groups, some having type I reaction centers (RCI in monoderm phylum Firmicutes; and diderm phyla Acidobacteria and Chlorobi), others with type II reaction centers (RCII in monoderm phylum Chloroflexi; and diderm taxa Gemmatimonadetes, and alpha-, beta-, and gamma-Proteobacteria), and some containing both (RCI and RCII, only in diderm phylum Cyanobacteria). In most bacterial phylograms, photosystem types and diderm taxa are polyphyletic. A more parsimonious arrangement, which is supported by photosystem evolution, as well as additional sets of molecular characters, suggests that endosymbiotic events resulted in the formation of the diderms. In the model presented, monoderms readily form a monophyletic group, while diderms are produced by at least two endosymbiotic events, followed by additional evolutionary changes.

Ginseng rusty root (GRR) symptom is one of the primary diseases of ginseng. There has been a problem of ginseng rusty root, leading to a severe decline in the quality of ginseng. To clarify the relationship between root symptoms of ginseng rust and soil, the physical and chemical properties, enzyme activity, community structure and microbial diversity of GRR and healthy ginseng (HG) rhizosphere soil were analyzed and compared. The pH and redox potential (Eh) of GRR soil decreased, and the contents of total phosphorus (TP), available phosphorus (AP), and available potassium (AK) decreased. The activity of catalase and phosphatase and invertase was lower than that of HG groups. Besides, the microbial community of GRR rhizosphere soil changes much, and its abundance and diversity are significantly reduced. The community structure of GRR rhizosphere soil also shows apparent differences, and the samples of the HG group gathered together, and the samples of the GRR group were dispersed. In general, GRR was closely associated with decreases in soil pH and Eh; decreases in TP, AP, and AK; decreases in the activity of several enzymes. Additionally, it is strongly associated with an increase in pathogenic microorganisms such as Ilyonectria and a reduction of beneficial microorganisms such as Tremellomycetes Acidobacteria subgroup 6 and Gemmatimonadetes.

Continuous cropping of tomato is increasingly practiced in greenhouse cultivation, leading to several soil-related obstacles. In this study, a type of microbial restoration substrate (MRS) was used to amend soils from the re-cropping of tomato for 8 years under greenhouse-cultivated conditions. Two treatments were established: using 1,500 kg hm−2 of MRS to amend soil as treatment (TR), and non-MRS as control (CK). The severity of bacterial wilt (BW), soil properties and rhizobacterial community composition under two different treatments were compared. The application of MRS led to an average 83.75% reduction in the severity of BW, and significantly increased the plant height, root activity and yield. Meanwhile, soil pH, soil organic contents (SOC), total nitrogen (TN) and exchangeable calcium were significantly increased (P

Soil bacteria are widely recognized for their roles in nutrient cycling, such as for nitrogen and phosphorus, and for promoting soil health. However, the relationship between soil bacteria and the availability of calcium, magnesium, iron, manganese, copper and zinc under different climatic conditions in orchard systems remains poorly understood. Here, we explored the relationship between soil bacteria and metal nutrient availability and uptake by apple trees based on 36 soil samples from three climate zones that span the major apple-producing areas in China. The results indicated that six phyla (e.g., Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, and Proteobacteria) in the soil bacterial communities were positively related to the metal nutrients availability, especially to calcium (16 OTUs) and magnesium (19 OTUs). At the class level, Alphaproteobacteria improved the availability of calcium, magnesium, iron, manganese and copper, while Actinobacteria improved the availability of zinc and altered absorption by the roots and the contents in leaves. We found that the underground bacterial community diversity was determined by climatic conditions and soil properties, which altered the effect of bacteria on soil metal nutrients availability, and led to differences of nutritional content in the aboveground plant portions. Therefore, soil bacteria played a central role in this process for sustainable development in apple orchard systems.

Complex building premises plumbing systems provide an ideal niche for diverse waterborne microorganisms, including opportunistic pathogens such as Legionella pneumophila. In this field study, we collected cold and hot water samples from premises plumbing systems of nine different high-rise buildings and examined the L. pneumophila culturable positivity and concentration to examine microbial ecology trends associated with L. pneumophila colonization. In addition, bacterial community structure was evaluated using high throughput 16S rRNA gene sequencing. 9.1% (2/22) of cold-water samples and 30.5% (18/59) of hot water samples were positive for L. pneumophila culture. 16S rRNA gene sequencing demonstrated a diverse bacterial community in the sampled premises plumbing systems. The phyla Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Thermi represented a combined 97.7% average relative abundance, dominating the bacterial community. Also, an apparent bacterial community difference was observed between cold water and hot water. Interestingly, by examining cold water and hot water separately, we identified several bacterial taxa in the phyla Bacteroidetes, Gemmatimonadetes, and Acidobacteria were significantly enriched in L. pneumophila culture positive samples, while taxa in Proteobacteria were significantly enriched in L. pneumophila culture negative water samples. The correlation of L. pneumophila colonization and bacterial community structure suggests a potential association between this waterborne opportunistic pathogen and the premises plumbing microbial community, which merits further research.

Verticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.

Elevational gradients strongly affect the spatial distribution and structure of soil bacterial communities. However, our understanding of the effects and determining factors is still limited, especially in the deep soil layer. Here, we investigated the diversity and composition of soil bacterial communities in different soil layers along a 1,500-m elevational gradient in the Taibai Mountain. The variables associated with climate conditions, plant communities, and soil properties were analyzed to assess their contributions to the variations in bacterial communities. Soil bacterial richness and α-diversity showed a hump-shaped trend with elevation in both surface and deep layers. In the surface layer, pH was the main factor driving the elevational pattern in bacterial diversity, while in the deep layer, pH and soil carbon (C) availability were the two main predictors. Bacterial community composition differed significantly along the elevational gradient in all soil layers. In the surface layer, Acidobacteria, Delta-proteobacteria, and Planctomycetes were significantly more abundant in the lower elevation sites than in the higher elevation sites; and Gemmatimonadetes, Chloroflexi, and Beta-proteobacteria were more abundant in the higher elevation sites. In the deep layer, AD3 was most abundant in the highest elevation site. The elevational pattern of community composition co-varied with mean annual temperature, mean annual precipitation, diversity and basal area of trees, pH, soil C availability, and soil C fractions. Statistical results showed that pH was the main driver of the elevational pattern of the bacterial community composition in the surface soil layer, while soil C fractions contributed more to the variance of the bacterial composition in the deep soil layer. These results indicated that changes in soil bacterial communities along the elevational gradient were driven by soil properties in both surface and deep soil layers, which are critical for predicting ecosystem functions under future climate change scenarios.

Background Angelica sinensis (Oliv.) Diels (A. sinensis) is a Chinese herb grown in different geographical locations. It contains numerous active components with therapeutic value. Rhizosphere microbiomes affect various aspects of plant performance, such as nutrient acquisition, growth and development and plant diseases resistance. So far, few studies have investigated how the microbiome effects level of active components of A. sinensis. This study investigated whether changes in rhizosphere microbial communities and metabolites of A. sinensis vary with the soil microenvironment. Soils from the two main A. sinensis-producing areas, Gansu and Yunnan Province, were used to conduct pot experiments. The soil samples were divided into two parts, one part was sterilized and the other was unsterilized planting with the seedling variety of Gansu danggui 90–01. All seedlings were allowed to grow for 180 days. At the end of the experiment, radix A. sinensis were collected and used to characterize growth targets and chemical compositions. Rhizosphere soils were subjected to microbial analyses. Results Changes in metabolic profiles and rhizosphere microbial communities of A. sinensis grown under different soil microenvironments were similar. The GN (Gansu non-sterilized), YN (Yunnan non-sterilized), GS (Gansu sterilized), and YS (Yunnan sterilized) groups were significantly separated. Notably, antagonistic bacteria such as Sphingomonas, Pseudomonas, Lysobacter, Pseudoxanthomonas, etc. were significantly (p Pseudomonas parafulva; organic acids (including chlorogenic acid, dicaffeoylquinic acid and 5-feruloylquinic acid) and their ester coniferyl ferulate which were enriched in YS Group were positively associated with Gemmatimonadetes bacterium WY71 and Mucilaginibater sp., respectively. Conclusions The soil microenvironment influences growth and level/type of active components in A. sinensis. Further studies should explore the functional features of quality-related bacteria, identify the key response genes and clarify the interactions between genes and soil environments. This will reveal the mechanisms that determine the quality formation of genuine A. sinensis.

This study explored variations in the rhizosphere microbial community composition resulting from the continuous cropping of sorghum. We explored the potential growth-promoting effects of Bacillus amyloliquefaciens in manipulating the microbial community composition of the rhizosphere soil under continuous cropping. Illumina MiSeq sequencing was used to compare the composition of the bacterial and fungal communities in the rhizosphere soil from a sorghum–maize rotation system, sorghum continuous cropping system, and sorghum continuous cropping with the application of the biological agent B. amyloliquefaciens. The rhizosphere soil under continuous sorghum cropping had lower bacterial richness and higher fungal diversity than the sorghum–maize rotation rhizosphere soil. The bacterial phyla Acidobacteria and Gemmatimonadetes, and the fungal phylum Basidiomycota, were strongly enriched in the continuous cropping soil. The class Tremellomycetes was the most dominant group, accounting for 19.30% of the total fungal sequences in the continuous cropping soil and 4.51% in sorghum-maize rotation soil. Application of B. amyloliquefaciens significantly decreased the abundance of Tremellomycetes by 8.87% in the continuous cropping soil. Our results indicate that the decrease in sorghum growth and yield under continuous cropping are in coincidence with the alteration of soil microbial community composition, particularly the accumulation of Tremellomycetes in the continuously cropped rhizosphere soil. Our findings contribute to an improved understanding of the effects of continuous sorghum cropping on soil microbiome, and B. amyloliquefaciens can be used to manipulate the microbial communities of the sorghum rhizosphere soil.

Red kidney bean (RKB) is an important cash crop of the Western Indian Himlayan (WIH) regions. Despite of having a long cultivation history, very little has known about its rhizospheric microbial diversity, which is becoming important for employing sustainable agricultural plans. In this perspective, the bacterial diversity and community structure of Himalayan RKB rhizosphere were studied and compared across the altitudinal zones of WIH. Metagenomic analysis revealed that Proteobacteria (31%) was the major phylum with the dominance of the genera Sphingomonas in the Garhwal while Pseudomonas in the Kumaun regions of Western Indian Himalaya (WIH), followed by Bacteroidetes (20%), Fermicutes (9%), Acidobacteria (7%), Actinobacteria (6%), Chloroflexi (5%), Gemmatimonadetes (3%) and Planctomyces (2%). Furthermore, the Garhwal soil was found to harbor more bacterial diversity than the Kumaun with unique genera Conexibacter, Ornithobacterium, Lacibacter, Salinibacter, Fervidicola, Haliangium, Pirellula, Caloramator, Desulfitobacterium, Edaphobacter, Holophaga and Massilia. The principal component analysis revealed that the bacterial diversity was associated with the content of “total solids” as well as “volatile acids” present in the respective soils. Additionally, large number of unclassified clone sequences suggesting the need of culture dependent studies to trap “yet not cultivated” bacterial species. Conclusively, the present study provides an overview of RKB associated bacterial diversity which must be explored for sustainable hill agricultural plans.

Effects of transgenic crops on soil microbial communities are important constituents in ecological risk assessment. The Illumina MiSeq sequencing method was employed to examine the effects of transgenic glufosinate-resistant rapeseed and the associated herbicide application on rhizospheric bacterial communities at different growth stages. Our results showed that both transgenic rapeseed and the application of herbicide Basta (active ingredient: glufosinate) had no significant influence on alpha-diversity of rhizospheric bacterial communities. The dominant phyla across all samples were Proteobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes and Actinobacteria. These dominant phyla show no remarkable differences under transgenic rapeseed, transgenic rapeseed with glufosinate applied, and non-transgenic acceptor counterpart rapeseed. Nevertheless, they respond differently at different growth stages. These results indicate that community variation was strongly dependent on the growth stage. Therefore, growing glufosinate-resistant transgenic rapeseed line Z7B10 and application of glufosinate herbicide had no adverse effects on the rhizospheric bacterial community composition.

Objective: Maize is an important crop for fodder, food and feed industry. The present study explores the plant-microbe interactions as alternative eco-friendly sustainable strategies to enhance the crop yield. Methodology: Bacterial diversity was studied in the rhizosphere of maize by culture-dependent and culture-independent techniques by soil sampling, extraction of DNA, amplification of gene of interest, cloning of desired fragment and library construction. Results: Culturable bacteria were identified as Achromobacter, Agrobacterium, Azospirillum, Bacillus, Brevibacillus, Bosea, Enterobacter, Microbacterium, Pseudomonas, Rhodococcus, Stenotrophomonas and Xanthomonas genera. For culture-independent approach, clone library of 16S ribosomal RNA gene was assembled and 100 randomly selected clones were sequenced. Majority of the sequences were related to Firmicutes (17%), Acidobacteria (16%), Actinobacteria (17%), Alpha-Proteobacteria (7%), Delta-proteobacteria (4.2%) and Gemmatimonadetes (4.2%) However, some of the sequences (30%) were novel that showed no homologies to phyla of cultured bacteria in the database. Diversity of diazotrophic bacteria in the rhizosphere investigated by analysis of PCR-amplified nifH gene sequence that revealed abundance of sequences belonging to genera Azoarcus (25%), Aeromonas (10%), Pseudomonas (10%). The diazotrophic genera Azotobacter, Agrobacterium and Zoogloea related nifH sequences were also detected but no sequence related to Azospirillum was found showing biasness of the growth medium rather than relative abundance of diazotrophs in the rhizosphere. Conclusion: The study provides a foundation for future research on focussed isolation of the Azoarcus and other diazotrophs found in higher abundance in the rhizosphere. Keywords: Azospirillum, Diazotrophs, 16S rRNA, nifH, Metagenomics

Soil microbial community composition and diversity were significantly affected by tree species, growth stage and soil nutrients in the forest ecosystem. We analyzed the bulk and rhizosphere soil microbial communities associated with young (20 year) and old (1000 year) trees of Platycladus orientalis using 16S and ITS rRNA high-throughput gene sequencing techniques. Platycladus orientalis growth altered the nutrient and microbial community compositions in the bulk and rhizosphere soils. In a typing analysis, the bacterial and fungal communities clustered into two and three groups, respectively, and only the fungal diversity exhibited significant differences between the bulk and rhizosphere soils. Soil microbial community compositions in bulk and rhizosphere soils were dominated by Acidobacteria, Proteobacteria, Actinobacteria and Ascomycota phyla, and their changes were driven by the Gemmatimonadetes, Nitrospirae, Planctomycetes, Zygomycota and Basidiomycota phyla. Compared with soils under young trees, 24.63% and 72.80% of the bacterial and fungal genera in bulk soil and 24.78% and 59.92% of the bacterial and fungal genera in rhizosphere soil shifted in the old trees samples. Soil microbial community compositions were sensitive to changes of soil nutrients, which explained 82.10% and 86.79% of the total variation in the major bacterial and fungal genera community compositions, respectively. Our results suggest that long-term growth of Platycladus orientalis trees significantly altered bulk and rhizosphere microbial community compositions, and its influence was greater on the fungal community than on the bacterial community.

Dwarf bunt of wheat, which is caused by Tilletia controversa J.G. Kühn, is a soil-borne disease which may lead up to an 80% loss of yield together with degradation of the quality of the wheat flour by production of a fishy smell. In this study, high-throughput sequencing technology was employed to characterize the microbial composition of wheat tissues (roots, spikes, first stem under the ear, and stem base) and rhizosphere soil of wheat varieties that are resistant and susceptible to T. controversa. We observed that the soil fungal community abundance and diversity were higher in resistant varieties than in susceptible varieties in both inoculated and uninoculated wheat, and the abundances of Sordariomycetes and Mortierellomycetes increased in the resistant varieties infected with T. controversa, while the abundances of Dothideomycetes and Bacteroidia increased in the susceptible varieties. Regarding the bacteria present in wheat tissues, the abundances of Chloroflexi, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Acidobacteria in the ear and the first stem under the ear were higher than those in other tissues. Our results indicated that the abundances of Sordariomycetes, Mortierellomycetes, Leotiomycetes, Chryseobacterium and Massilia were higher in T. controversa-infected resistant varieties than in their controls, that Dothideomycetes, Bacteroidia, Nocardioides and Pseudomonas showed higher abundances in T. controversa-infected susceptible varieties, and that Curtobacterium, Exiguobacterium, Planococcus, and Pantoea may have higher abundances in both T. controversa-infected susceptible and resistant varieties than in their own controls.

Background Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. To investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during the maturity stage of three kinds of Dendrobium species. Results In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria. Conclusions We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

Soil salinization is an increasingly serious problem and decreases crop yields in the Yellow River Delta (YRD), but its effects on bacterial community and diversity at the phylum level are not well known. We used high-throughput sequencing of soil bacterial 16S rRNA to identify soil bacterial communities and diversity across a gradient of soil salinity (electrical conductivity), namely, S1: low salinity level (1.78 ds/m), S2: medium salinity level (3.16 ds/m), S3: high salinity level (17.26 ds/m), S4: extreme salinity level (34.41 ds/m), and a non-salted site as the control (CK, 0.92 ds/m). Our results indicated that CK, S2, S3, and S4 exhibited an increased soil C/N ratio of 0.64, 0.97, 1.27, and 1.55 times, respectively, compared with that in S1. Significantly lower values of the Shannon and Chao 1 indexes were observed in S4 compared with the CK (p < 0.05). High salinity decreased the relative abundance of Actinobacteria and Acidobacteria, but increased that of Gemmatimonadetes and Bacteroidetes. Additionally, the Shannon diversity of Bacteroidetes increased by 15.5% in S4 compared with that in the CK. Our results indicate that soil salt is a main factor regulating bacterial phyla diversity and community in the extremely saline-alkaline soils of YRD. The high abundance and diversity of Bacteroidetes can be used for saline-alkali land restoration.

13 páginas.- 4 figuras.- 3 tablas.- 60 referencias, The microbiota associated with vermiculations from karst caves is largely unknown. Vermiculations are enigmatic deposits forming worm-like patterns on cave walls all over the world. They represent a precious focus for geomicrobiological studies aimed at exploring both the microbial life of these ecosystems and the vermiculation genesis. This study comprises the first approach on the microbial communities thriving in Pertosa-Auletta Cave (southern Italy) vermiculations by next-generation sequencing. The most abundant phylum in vermiculations was Proteobacteria, followed by Acidobacteria > Actinobacteria > Nitrospirae > Firmicutes > Planctomycetes > Chloroflexi > Gemmatimonadetes > Bacteroidetes > Latescibacteria. Numerous less-represented taxonomic groups (< 1%), as well as unclassified ones, were also detected. From an ecological point of view, all the groups co-participate in the biogeochemical cycles in these underground environments, mediating oxidation-reduction reactions, promoting host rock dissolution and secondary mineral precipitation, and enriching the matrix in organic matter. Confocal laser scanning microscopy and field emission scanning electron microscopy brought evidence of a strong interaction between the biotic community and the abiotic matrix, supporting the role of microbial communities in the formation process of vermiculations., Open access funding provided by Università degli Studi di Salerno within the CRUI-CARE Agreement. This work was supported by Musei Integrati dell’Ambiente Foundation, by the Spanish project MINECO [CGL2016-75590-P] with European Regional Development Fund and by University of Salerno [ORSA197159].

The plant rhizosphere interfaces an array of microbiomes related to plant growth and development. Cultivar-specific soil microbial communities with respect to their taxonomic structure and specific function have not been investigated explicitly in improving the adaptation of lentil cultivars under rice-fallow ecology. The present study was carried out to decipher the rhizosphere microbiome assembly of two lentil cultivars under rice-fallow ecology for discerning the diversity of microbial communities and for predicting the function of microbiome genes related to nitrogen (N) and phosphorus (P) cycling processes deploying high-throughput whole (meta) genome sequencing. The metagenome profile of two cultivars detected variable microbiome composition with discrete metabolic activity. Cyanobacteria, Bacteroidetes, Proteobacteria, Gemmatimonadetes, and Thaumarchaeota were abundant phyla in the &ldquo, Farmer-2&rdquo, rhizosphere, whereas Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Chloroflexi, and some incompletely described procaryotes of the &ldquo, Candidatus&rdquo, category were found to be robustly enriched the rhizosphere of &ldquo, Moitree&rdquo, Functional prediction profiles of the microbial metagenomes between two cultivars revealed mostly house keeping genes with general metabolism. Additionally, the rhizosphere of &ldquo, had a high abundance of genes related to denitrification processes. Significant difference was observed regarding P cycling genes between the cultivars. &ldquo, with a profuse root system exhibited better N fixation and translocation ability due to a good &ldquo, foraging strategy&rdquo, for improving acquisition of native P under the nutrient depleted rice-fallow ecology. However, &ldquo, revealed a better &ldquo, mining strategy&rdquo, for enhancing P solubilization and further transportation to sinks. This study warrants comprehensive research for explaining the role of microbiome diversity and cultivar&ndash, microbe interactions towards stimulating microbiome-derived soil reactions regarding nutrient availability under rice-fallow ecology.

Soil microorganisms play an important role in determining productivity of agro-ecosystems. This study was conducted to compare diversity, richness, and structure (relative abundance at the phylum level) of soil bacterial communities among three rice-based cropping systems, namely, a winter fallow-rice-rice (FRR), green manure (Chinese milk vetch)-rice-rice (MRR), and oilseed rape-rice-rice (ORR), in which MRR and ORR had significantly higher productivity than FRR. A 16S rRNA gene sequence analysis showed that no significant differences were observed in diversity and richness indices (observed species, Shannon, Simpson, Chao1, abundance-based coverage estimators, and phylogeny-based metrics) of soil bacterial communities among the three cropping systems. However, relative abundances of dominant phyla in soil bacterial communities, including Proteobacteria, Acidobacteria, Nitrospirae, Gemmatimonadetes, and Verrucomicrobia, were significantly different among the three cropping systems. In particular, a significant reduction in the relative abundance of Nitrospirae was observed in both MRR and ORR compared with FRR. These results indicate that bacterial community structure was affected by cropping systems in the tested paddy soils. Based on the results of our studies and existing knowledge bases, we speculate that benefits to rice yield may be obtained by reducing the relative abundance of Nitrospirae and increasing the ratio of abundances of Proteobacteria/Acidobacteria in paddy soils.

Background Ferula sinkiangensis is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in regulating global biogeochemical cycle, plant growth and adaptability. However, the Ferula sinkiangensis bacterial community and the processes that drive its assembly remain unclear. Results In this study, based on Illumina HiSeq high-throughput sequencing, we explored the diversity, structure and composition of Ferula sinkiangensis rhizosphere bacterial communities at different slope positions (upper, middle and bottom) and soil depths (0-10 cm, 10-25 cm, 25-40 cm) and their correlation with soil physicochemical properties. Actinobacteria (22.7%), Proteobacteria (18.6%), Acidobacteria (14.0%), Gemmatimonadetes (10.1%), Cyanobacteria (7.9%), Bacteroidetes (6.9%), Planctomycetes (3.9%), Verrucomicrobia (3.5%), Firmicutes (3.4%) and Chloroflexi (3.2%) were the dominant bacterial phyla in Ferula sinkiangensis rhizosphere soil. Variance analysis showed that the diversity and abundance of rhizosphere bacterial community in Ferula sinkiangensis were significantly different at various slope positions and soil depths. Specifically, the diversity of bacterial community was significantly higher at the top than the bottom of the slope, and the diversity and richness of bacterial community were significantly greater in the 0-10cm than the 25-40cm soil layer. Linear discriminant effect size (LEfSe) analysis showed the specific phyla and genera of bacteria affected by slope position and soil depth. For example, Planctomycetes, Sphingomonas , Rubrobacter and Adhaeribacter by slope position and significant impact on soil depth. In addition, distance-based redundancy analysis (db-RDA) and variance analysis showed that soil physicochemical factors jointly explained 29.81% of variation in Ferula sinkiangensis rhizosphere bacterial community structure. There was a significant positive correlation between available phosphorus（AP）and the diversity of Ferula sinkiangensis rhizosphere bacterial community ( p < 0.01), whereas pH largely explained the variation of Ferula sinkiangensis rhizosphere bacterial community structure (5.58%, p < 0.01), followed by altitude (5.53%), total salt (TS, 5.21%) and total phosphorus (TP, 4.90%). Conclusion Our results revealed the heterogeneity and variation trends of Ferula sinkiangensis rhizosphere bacterial community diversity and abundance on a fine spatial scale (slope position and depth) and shed new light on the mechanisms of coevolution and interaction between Ferula sinkiangensis and their rhizosphere bacterial communities across environmental gradients.

Using high-throughput sequencing, we performed a full-profile analysis of the taxonomic structure and diversity of prokaryotic communities of zonal soil series: sod-podzolic, dark gray, typical chernozem, brown soil, meadow-chestnut soil and solonets. Phyla Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia formed up to 95% of prokaryotic communities in all studied soil horizons. Phyla Proteobacteria and Actinobacteria and archaeal phylum Thaumarchaeota dominated in all soils. We revealed the trends of changes in the representation of bacterial phyla in the soils of the zonal range from taiga to dry-steppe: a decrease of Acidobacteria and an increase of Actinobacteria in the upper horizons. The diversity indices of the prokaryotic communities of different genetic horizons of the studied soils were evaluated. In all soils, a decrease in diversity indices with the depth of the horizon was revealed. In all soils, a decrease in diversity indices with depth of the horizon was found, with a rare and slight increase in some lower horizons: structural metamorphic (BM), textural (BT) or accumulative carbonate (BCA) horizons. When examining the prokaryotic communities of soils with different genesis, no determining influence of pH and organic matter contents on the diversity indices was found. Differences in the taxonomic structure and diversity of prokaryotic communities of soils of different bioclimatic zones were presented due to a combination of factors: the difference in chemical and physical properties of soils, as well as in water and temperature conditions.

Compost amendment reportedly improved apple tree growth in replant soils. However, its effects should be evaluated at different soil depths and locations. This study investigated the impact of soil improvement with compost on soil physicochemical properties and bacterial community structure of a replanted apple orchard in comparison with the original orchard without compost improvement. The V1–V3 region of the bacterial 16S rRNA gene was subjected to high-throughput 454 pyrosequencing, and data were analyzed using the Mothur pipeline. The results showed that the soil improvement benefited tree growth and fruit quality during the study period. The compost amendment markedly increased tree height and stem diameter by a range of 6.1%–21.0% and 4.0%–14.0%, respectively. Fruit yield (9.5%), average weight (9.6%), and soluble solid content (5.6%) were also increased by compost amendment compared to those of the unimproved treatment. The pH, organic matter, and available N, P, and K contents were significantly increased by 5.7%–21.9%, 0.2%–62.9%, 9.3%–29.3%, 36.7%–64.5%, and 17.2%–100.3% in the compost improved soil. The pyrosequencing data showed that the soil improvement changed the bacterial community structure at all soil depths (0–20 cm and 20–40 cm) and locations (in-row and inter-row) considered; e.g., the relative abundance of Proteobacteria (20.2%), Bacteroidetes (2.5%), and Cyanobacteria (1.0%) was increased while that of Chloroflexi (5.5%), Acidobacteria (5.2%), Nitrospirae (4.5%), Gemmatimonadetes (3.8%), and Actinobacteria (1.8%) was decreased. The relative abundance of some dominant genera Burkholderia (2.3%), Pseudomonas (1.0%), and Paenibacillus (0.5%) were enhanced in the compost improved soil. Moreover, other dominant genera such as Nitrospira (6.4%), Gemmatimonas (2.2%), and Phenylobacterium (0.3%) were reduced by the application of compost. Our results indicate that soil improvement benefits the growth of tree and fruit quality, and is likely mediated by increased soil pH, organic matter, and available nutrient contents and beneficial bacterial community composition.

Angkor temples in Cambodia, an icon of Khmer civilization, display the ancient culture by bas-relief on the sandstone surface of different temples, which are being destroyed by physical, chemical and biological processes for more than a thousand years. To investigate the bio-erosion of temple sandstone at the Royal Palace of Angkor Thom and Beng Mealea in Cambodia, Next Generation Sequencing (NGS) Illumina sequencing technology based on 16S rRNA gene was performed on samples of biofilm and exfoliated sandstone materials to identify the microbial community composition. After quality filtering the raw data, 678,115 quality reads were obtained for bacterial 16S rRNA gene from a total of 13 samples with high Goods coverage and satisfactory rarefaction curves. Higher bacterial diversity was detected in exfoliated sandstone materials than the biofilms, but the lowest in the lower layers of the biofilm than the top layers. At the phylum level, 4 phyla, namely Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi, were the most common and dominant bacterial groups in these samples with each contributing to greater than 3.7% of the total abundance. Both Firmicutes and Gemmatimonadetes were the dominant phyla detected only in exfoliated materials, while Cyanobacteria, Chloroflexi, and unassigned bacteria were more abundant in the biofilms. Hierarchical cluster analysis at the genus level showed that the distribution of bacterial community composition between exfoliated materials and biofilms was significantly different. The microbiota of Beng Mealea and the Royal Palace was different, especially for the biofilm samples. The correlation of environmental factors and bacterial community structure suggested that the nitrification process was more active at Ben Mealea, which might contribute to biodeterioration. This analysis of microbiota in these biofilms and sandstone exfoliation materials provides further information on the responsible microorganisms involved in geobiochemical processes at Angkor monuments and preservation strategies under tropical climate conditions.

Forest rings are 50-1600 m diameter circular structures found in boreal forests around the globe. They are believed to be chemically reducing chimney features, having an accumulation of reduced species in the middle of the ring and oxidation processes occurring at the ring's edges. It has been suggested that microorganisms could be responsible for charge transfer from the inside to the outside of the ring. To explore this, we focused on the changes in bacterial and archaeal communities in the ring edges of two forest rings, the 'Bean' and the 'Thorn North' ring, in proximity to each other in Ontario, Canada. The drier samples from the methane-sourced Bean ring were characterized by the abundance of bacteria from the classes Deltaproteobacteria and Gemmatimonadetes. Geobacter spp. and methanotrophs, such as Candidatus Methylomirabilis and Methylobacter, were highly abundant in these samples. The Thorn North ring, centred on an H2 S accumulation in groundwater, had wetter samples and its communities were dominated by the classes Alphaproteobacteria and Anaerolineae. This ring's microbial communities showed an overall higher microbial diversity supported by higher available free energy. For both rings, the species diversity was highest near the borders of the 20-30 m broad ring edges.

Climate change contributes to drought stress and subsequently affects crop growth, development, and yield. The microbial community, such as fungi and bacteria in the rhizosphere, is of special importance to plant productivity. In this study, soil collected from a cotton research field was used to grow cotton plants (Gossypium hirsutum cv. Jin668) under controlled environment conditions. Drought stress was applied at flowering stage, while control plants were regularly watered. At the same time, the soil without plants was also subjected to drought, while control pots were regularly watered. The soil was collected in sterilized tubes and microbial DNA was isolated and high-throughput sequencing of 16S rRNA genes was carried out. The alpha diversity of bacteria community significantly increased in the soil with cotton plants compared to the soil without cotton plants. Taxonomic analysis revealed that the bacterial community structure of the cotton rhizosphere predominantly consisted of the phyla Proteobacteria (31.7%), Actinobacteria (29.6%), Gemmatimonadetes (9.8%), Chloroflexi (9%), Cyanobacteria (5.6%), and Acidobacteria. In the drought-treated rhizosphere, Chloroflexi and Gemmatimonadetes were the dominant phyla. This study reveals that the cotton rhizosphere has a rich pool of bacterial communities even under drought stress, and which may improve drought tolerance in plants. These data will underpin future improvement of drought tolerance of cotton via the soil microbial community.

The Buda Thermal Karst System (BTKS) is an extensive active hypogenic cave system located beneath the residential area of the Hungarian capital. At the river Danube, several thermal springs discharge forming spring caves. To reveal and compare the morphological structure and prokaryotic diversity of reddish-brown biofilms developed on the carbonate rock surfaces of the springs, scanning electron microscopy (SEM), and molecular cloning were applied. Microbial networks formed by filamentous bacteria and other cells with mineral crystals embedded in extracellular polymeric substances were observed in the SEM images. Biofilms were dominated by prokaryotes belonging to phyla Proteobacteria, Chloroflexi and Nitrospirae (Bacteria) and Thaumarchaeota (Archaea) but their abundance showed differences according to the type of the host rock, geographic distance, and different water exchange. In addition, representatives of phyla Acidobacteria, Actinobacteria, Caldithrix, Cyanobacteria, Firmicutes Gemmatimonadetes, and several candidate divisions of Bacteria as well as Crenarchaeota and Euryarchaeota were detected in sample-dependent higher abundance. The results indicate that thermophilic, anaerobic sulfur-, sulfate-, nitrate-, and iron(III)-reducing chemoorganotrophic as well as sulfur-, ammonia-, and nitrite-oxidizing chemolithotrophic prokaryotes can interact in the studied biofilms adapted to the unique and extreme circumstances (e.g., aphotic and nearly anoxic conditions, oligotrophy, and radionuclide accumulation) in the thermal karst springs.

In this study, the sequencing of 16S ribosomal DNA was used to characterize the soil bacterial community composition and diversity in Liaohe estuarine wetland. Soil samples were taken from different locations in the wetland dominated by reed. Moreover, the soil quality parameters were evaluated (pH, moisture, organic matter, total nitrogen, available nitrogen, total phosphorus, available phosphorus). The results showed that the organic matter and nutrient contents were significantly higher in irrigated wetland than those in natural wetland. Major phylogenic groups of bacteria in soil samples including Proteobacteria, Acidobacteria, Gemmatimonadetes, Actinobacteria and Cyanobacteria were analyzed and we found that Proteobacteria was the most abundant in the community, and the phylum Acidobacteria was more abundant in irrigated wetland. Beta diversity analyses indicated that the soil bacterial community was mainly affected by sampling sites rather than seasons. In general, the bacterial community in natural wetland was not significantly different with that in artificial irrigated wetland. Artificial hydraulic engineering irrigated according to the water requirement rule of reed, increased the production of reeds, changed the way of wetland soil material input, but the diversity of bacterial community kept stable relatively.

Globally, the rate and extent of cropland abandonment increase greatly since 1950s. Knowledge of soil bacteria and fungi succession during long-term vegetation development is particularly limited for the abandoned croplands. In order to test the effects of agricultural abandonment on soil biota succession, we studied the soil bacterial and fungal composition and diversity in abandoned farmlands across a century of secondary vegetation successional gradient in China’s Qinling Mountains. Using high-throughput sequencing technologies, the soil fungal and bacterial communities were studied in 22 abandoned farmlands, as well as 7 adjacent arable fields representing non-abandoned references. The stand age, i.e., years since agricultural abandonment, affected the soil bacterial and fungal composition and explained 8.7 and 31.6% variations of bacterial and fungal communities (at order level), repectively. The Proteobacteria, dominated by chemoorganotrophic bacteria, kept its absolute dominance status (38.66% - 40.77%) constantly during succession even though the vegetation changed obviously from crop to grass, shrub, and forest. The relative abundances of Acidobacteria, Planctomycetes, Verrucomicrobia, Nitrospirae, and Spirochaetes increased significantly with stand age (i.e., years since abandonment), while the Firmicutes, Actinobacteria, Gemmatimonadetes, Cyanobacteria, and Armatimonadetes showed an opposite trend. A distinct shift in fungal communities from Ascomycota -dominant in young stands to Basidiomycota -dominant in older stands was observed, which could be attributed to the increase of vegetation coverage and soil moisture during succession. The soil bacterial richness and diversity increased logarithmically with increasing stand age and gradually reached equilibrium in late-successional stage. Soil fungal diversity tended to increase in the early successional stages and then followed by a decreasing trend. The soil pH was the most important environmental factor predicating the soil fungal α-diversity measurements. Both the soil bacterial and fungal communities displayed successional trends along with vegetation succession. The soil bacteria and fungi exhibited marked differences in successional pattern during secondary succession following agricultural abandonment.

Bioremediation, is an effective and environment-friendly method of cleaning up crude oil pollution after an oil spill. However, the in situ bioremediation of crude oil is usually inhibited by deficiency of inorganic nutrients. To understand the effects of nutrient addition on the bioremediation of crude oil and the succession of bacterial communities during process of bioremediation, microcosms containing oil-contaminated sediments were constructed and biodegradation of crude oil was assessed based on the depletion of different ingredients. We used two culture-independent methods, denaturing gradient gel electrophoresis and a 16S rRNA gene based clone library, to analyze the succession of bacterial communities. The results suggested n-alkanes were degraded after 30 days and that nutrient amendments significantly improved the efficiency of their biodegradation. Moreover, oil contamination and nutrient amendments could dramatically change bacterial community structures. Lower diversity was detected after being contaminated with oil. For instance, bacterial clones affiliated with the phylum Armatimonadetes, Firmicutes, Gemmatimonadetes, and Planctomycetes and the class Deltaproteobacteria and Epsilonproteobacteria could not be identified after 30 days of incubation with crude oil. However, “professional hydrocarbonocastic bacteria” became abundant in samples treated with oil during the bioremediation period, while these clones were almost completely absent from the control plots. Interestingly, bioinformatics analysis showed that even when dramatic differences in oil biodegradation efficiency were observed, bacterial communities in the plots with nutrient amendments were not significantly different from those in plots treated with oil alone. These findings indicated that nutrient amendments could stimulate the process of biodegradation but had less impact on bacterial communities. Overall, nutrient amendments might be able to stimulate the growth of n-alkane degrading bacteria.

Soil microorganisms play critical roles in maintaining ecological functions of the northern mixed-grass prairie. While defoliation regimes and elevated precipitation affect plant community composition and primary productivity in these grasslands, their effects on soil microbiome and interactome have not been studied. We examined the response of soil microbiome and interactome to long-term (2010–2015) treatments of varying defoliation regimes (low vs. high intensity and low vs. high frequency) and two precipitation conditions (ambient vs. elevated) on two contrasting sites (a dry vs. a mesic site) in a northern mixed-grass prairie. High intensity defoliation reduced alpha-diversity and altered the beta-diversity of soil microbial communities in the mesic site but not in the dry site, while elevated precipitation reduced alpha-diversity and altered the beta-diversity of soil microbial communities in both sites. Defoliation and precipitation did not show interaction effects on overall alpha- and beta-diversity, but did combine to influence the interactome network. High intensity defoliation promoted the oligotrophic genera Spartobacteria (Verrucomicrobia), Pseudonocardia (Actinobacteria), and Conexibacter (Actinobacteria), while elevated precipitation promoted the copiotrophic genera Nitrososphaera (Thaumarchaeota), Anderseniella (Proteobacteria), Sphingomonas (Proteobacteria), and Acidobacteria Gp16 (Acidobacteria). High intensity defoliation increased the number of linkages for Alphaproteobacteria and Acidobacteria, and decreased the number of linkages for Gemmatimonadetes and Spartobacteria in the interactome networks. However, elevated precipitation increased the number of linkages for Actinobacteria and Gemmatimonadetes and decreased the number of linkages for Spartobacteria and Acidobacteria. Our results show that defoliation intensity and elevated precipitation affected the microbiome and associated interactome network within soils of the northern mixed-grass prairie by affecting different functional taxonomic groups, indicating distinct scenarios for defoliation and precipitation in affecting soil microbial communities.

Aims To reveal the relationship of the bacterial communities in shrimp intestine and surrounding environments. Methods and results We examined bacterial communities in the intestine of pacific white shrimp, Litopenaeus vannamei, the surrounding water and sediment by high-throughput sequencing analysis. Sequences were clustered into operational taxonomic units (OTUs) at 97% similarity levels, which ranged from 4956 to 5976 in each sample. All OTUs were affiliated with at least 64 phyla. The 10 most abundant phyla were Proteobacteria, Cyanobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Acidobacteria, Actinobacteria, Planctomycetes, Gemmatimonadetes and Verrucomicrobia. The relationship of bacterial communities in the intestine and the surroundings was also investigated. A total of 1395 OTUs shared in the three habitats, accounting for 80, 65 and 77% in the intestine, the surrounding water and sediment respectively. There were 352, 891, 833 unique OTUs in intestine, surrounding water and sediment. Welch's t-test analysis showed that the abundances of some taxa were significantly different between the shrimp intestine and surroundings. Unweighted pair-group method with arithmetic mean analysis revealed that there was a generally similar bacterial community composition in three environments. Conclusions These results showed that the bacterial compositions are mostly the same in shrimp intestine, water and sediment, but with different relative abundances of the bacterial communities. Significance and impact of the study This study provided valuable findings on the relationship of the bacterial communities in shrimp intestine, the surrounding water and sediment, which can expand our knowledge of the broad trend on bacterial community in shrimp cultural ecosystems.

© 2018 Macmillan Publishers Ltd., part of Springer Nature. In soil ecosystems, microorganisms produce diverse secondary metabolites such as antibiotics, antifungals and siderophores that mediate communication, competition and interactions with other organisms and the environment1,2. Most known antibiotics are derived from a few culturable microbial taxa3, and the biosynthetic potential of the vast majority of bacteria in soil has rarely been investigated4. Here we reconstruct hundreds of near-complete genomes from grassland soil metagenomes and identify microorganisms from previously understudied phyla that encode diverse polyketide and nonribosomal peptide biosynthetic gene clusters that are divergent from well-studied clusters. These biosynthetic loci are encoded by newly identified members of the Acidobacteria, Verrucomicobia and Gemmatimonadetes, and the candidate phylum Rokubacteria. Bacteria from these groups are highly abundant in soils5-7, but have not previously been genomically linked to secondary metabolite production with confidence. In particular, large numbers of biosynthetic genes were characterized in newly identified members of the Acidobacteria, which is the most abundant bacterial phylum across soil biomes5. We identify two acidobacterial genomes from divergent lineages, each of which encodes an unusually large repertoire of biosynthetic genes with up to fifteen large polyketide and nonribosomal peptide biosynthetic loci per genome. To track gene expression of genes encoding polyketide synthases and nonribosomal peptide synthetases in the soil ecosystem that we studied, we sampled 120 time points in a microcosm manipulation experiment and, using metatranscriptomics, found that gene clusters were differentially co-expressed in response to environmental perturbations. Transcriptional co-expression networks for specific organisms associated biosynthetic genes with two-component systems, transcriptional activation, putative antimicrobial resistance and iron regulation, linking metabolite biosynthesis to processes of environmental sensing and ecological competition. We conclude that the biosynthetic potential of abundant and phylogenetically diverse soil microorganisms has previously been underestimated. These organisms may represent a source of natural products that can address needs for new antibiotics and other pharmaceutical compounds.

This study aimed to investigate the endophytic bacterial communities among various rice seed genotypes, to define the core microbiome and to further explore the relationship between rice genotypes and their endophytic bacterial flora. Simple sequence repeats molecular marker technology was used to investigate the genetic polymorphism in five different genotypes of rice. Endophytic bacterial communities in rice seeds were investigated using the Illumina-based 16S rRNA gene. The results showed that rice genotype had little impact on the diversity and richness of endophytic bacteria in seeds. The various rice genotypes do not have significantly different communities of endophytic bacterial in seeds, but the endophyte abundance distributions are obviously different, especially the dominant endophytic genera. Some phyla, such as Acidobacteria, Fusobacteria, Chlamydiae and Gemmatimonadetes, were first detected in rice seeds using high-throughput sequencing technique. As expected, five different rice genotypes were found to have a shared microbiome. At the genus level, Pantoea (28.33–72.77%), Acinetobacter (0.16–34.23%) and Xanthomonas (3.20–13.51%), which are probably the core microflora in indica rice seeds, served as the dominant genera that coexisted in all rice seeds tested. However, the current studies cannot confirm the correlation of rice phylogeny and seed bacterial microbiome clearly, but provide some clues of technical possibility and valuable experiences for the future study.

As the scale and intensity of mining increase, the application of mineral agents raises concerns about its environmental impact, but little information is available on the combined toxic effect of cresol frothing agent and Cu2+ on the soil microbial activity. In this work, microcalorimetric method, enzyme activity and Illumina HiSeq 2500 high throughput sequencing technology were combined to determine the effect of binary toxicants on soil microorganisms. The dose-toxicity relationship obtained from microcalorimetry experiments indicated that an increase in dosage was associated with a decrease in metabolic rate constant k (or an increase in the inhibitory ratio). The ratio of 400/0.08 (mg·L−1/mg·g−1) of Cu2+/cresols stimulated the growth of microorganisms in soil. Urease and fluorescein diacetate esterase activities upon the exposure of binary toxic mixture showed a negative impact and the toxicity order followed: Cu2+/p-cresol > Cu2+/o-cresol > Cu2+/m-cresol. By Illumina HiSeq 2500 high throughput sequencing technology, the results of microbial communities in 3 soil samples showed no significant differences, and Proteobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes phyla were the dominant species as Gram-negative bacteria.

The Israeli Mediterranean ecosystem has a distinctive flora with high levels of plant diversity. Previous studies of soil microbial ecology from the region have paid little attention to the possibility of distinctive soil bacterial communities associated with particular habitats. This study looked at bacterial communities present in the bulk soil from the closed canopy of four indigenous plants – Quercus ithaburensis, Calicotome villosa, Sarcopoterium spinosum , and Rhamnus puncata . Soil DNA was amplified for the 16S rRNA gene and sequenced using MiSeq Illumina platform. Results indicated that the bacterial communities differed between open and closed canopy with no significant difference in community structure within closed canopy, with soil moisture and organic matter content significantly influenced the community. Only the relative abundance of Gemmatimonadetes varied significantly with the open canopy having the highest abundance, and the relative abundance of Spartobacteri a and Saprospirae was unusually high compared to other Mediterranean soils. There was no difference in OTU richness between plant species. Additionally, this study revealed that open canopy community between plants was nested within closed canopy bacterial community implying that open canopy community potentially serves as a source for the closed canopy. It is then possible that the rhizospheric influence extends beyond the root-soil interface and to the surrounding bulk soil. Overall, this study indicates that in Israeli Mediterranean ecosystems native plants extend a selection beyond the rhizosphere, and like other studies from Mediterranean ecosystems pH does not seem to play an integral role in structuring bacterial communities.

The use of fertilizers to overcome nutrient constraints is standard practice in Paulownia fortunei plantations to increase stem wood production and tree yields. However, little is known about the responses and important role of the soil bacteria involved in the increases of soil fertility and standing volume with different fertilization. The 16S rRNA was used to compare four different fertilizer treatments for soil bacterial communities in three P. fortunei plantations, in Hunan Province, China. The results showed that the soil bacteria richness was significantly higher in plantations fertilized for ten years than for shorter times. The phyla Acidobacteria and Gemmatimonadetes were more prevalent for ten-year old plantations, and Firmicutes significantly increased with organic manure treatment (denoted as OM; p

Clubroot is an infection of cruciferous crops which results in considerable yield losses, caused by Plasmodiophora brassicae Woron. Bacillus subtilis XF-1 isolated from the rhizosphere of Chinese cabbages with severe clubroot in Guandu District of Kunming, Yunnan Province, China, has strong inhibitory effects on the resting spores of P. brassicae. However, its potential effects on the soil bacterial and fungal communities are still unknown. In this study, B. subtilis XF-1 was inoculated into cabbage rhizosphere and incidence of clubroot disease was surveyed, furthermore, an effect of this strain on soil microbial community in cabbage rhizosphere was investigated using Biolog™ MicroPlates and 454 pyrosequencing. B. subtilis XF-1 reduced the disease index (DI) by 17.14% and the control efficiency was 76.92%. The results of Biolog analysis and high-throughput pyrosequencing demonstrated that Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Gemmatimonadetes were the dominant taxonomic phyla found among bacteria in ten samples and Ascomycota, Basidiomycota and early diverging fungal lineages were reported among fungi. The soil bacterial and fungal communities were reduced greatly at the beginning, but they were recovered gradually with the growth of plant. However, there was little difference between treatment and control at the mature stage. The present study demonstrated that the effect of B. subtilis XF-1 on soil fungal community in cabbages rhizosphere was just transient and that the high-throughput 454 pyrosequencing is a suitable method for the characterization of microbial communities of rhizosphere soil of cabbage.

The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, “Ca. Marinimicrobia” (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and “Ca. Woesearchaeota” (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.

Microbiomes were analyzed in samples of the major soil types of Russia and Western Kazakhstan region from different plant communities (fallow, forest, agrophytocenosis). The representatives of 42 bacterial and 2 archaeal phyla were identified in the samples, among which the dominant positions were occupied by representatives of ten phyla: nine bacterial (Actinobacteria (33.5%), Proteobacteria (28.4%), Acidobacteria (8.3%), Verrucomicrobia (7.7%), Bacteroidetes (4.2%), Chloroflexi (3.0%), Gemmatimonadetes (2.3%), Firmicutes (2.1%), Planctomycetes (2.0%)) and one archaeal Crenarchaeota (2.6%). Data analysis by the methods of multivariate statistics suggests that the taxonomic structure of microbiota is formed under the action of two main factors: the strongest factor is soil acidity, which determines the dynamics of the microbiome at the level of major taxa such as phylum, and the weaker factor is the type of vegetation, which determines the community structure at lower taxonomic level (order, family, genus). Detailed analysis of the samples of podzolic soil in Leningrad Region made it possible to identify bacterial taxa specifically associated both with the type of biome (fallow, forest, agrophytocenosis) and with the specific plant community (specific composition of plant synusia).

The rapid development of high-throughput techniques and expansion of bacterial databases have accelerated efforts to bring plant microbiomes into cultivation. We introduced plant-only-based culture media as a successful candidate to mimic the nutritional matrices of plant roots. We herein employed a G3 PhyloChip microarray to meticulously characterize the culture-dependent and -independent bacterial communities of the maize root compartments, the endo- and ecto-rhizospheres. An emphasis was placed on the preference of the growth of unculturable candidate divisions/phyla on plant-only-based culture media over standard culture media (nutrient agar). A total of 1,818 different operational taxonomic units (OTUs) were resolved representing 67 bacterial phyla. Plant-only-based culture media displayed particular affinity towards recovering endophytic over ectophytic rhizobacteria. This was shown by the slightly higher recovery of CFUs for endophytes on plant-only-based culture media (26%) than on standard culture media (10%) as well as the higher taxa richness and numbers of exclusive families of unculturable divisions/phyla. Out of 30 bacterial phyla (comprising >95% of the whole population), 13 were of a significantly higher incidence on plant-only-based culture media, 6 phyla of which were not-yet-cultured (Atribacteria, OP9; Dependentiae, TM6; Latescibacteria, WS3; Marinimicrobia, SAR406; Omnitrophica, OP3; BRC1). Furthermore, plant-only-based culture media significantly enriched less abundant and/or hard-to-culture bacterial phyla (Acidobacteria, Gemmatimonadetes, and Tenericutes). These results present conclusive evidence of the ability of plant-only-based culture media to bring the plant-fed in situ microbiome into the status of plant-fed in vitro cultures, and to widen the scope of cultivation of heretofore-unculturable bacterial divisions/phyla.

Potato and sugar beet, which are widely grown in southern Alberta, may degrade soil quality because they return little C to the soil, and their harvesting methods cause soil disturbance that increases erosion risk. To reverse these effects, a 12-yr study was established to evaluate soil conservation (CONS) management systems for rotations that included potato, sugar beet, dry bean and wheat. These systems, comprising addition of feedlot manure compost, reduced tillage, diverse crop rotations and use of cover crops, were applied to 3- to 5-yr crop rotations. They were compared with conventional (CONV) management systems that did not have any of the CONS practices. In the final year of the study, pyrosequencing was used to determine differences in soil bacterial community profiles between the two systems (CONS vs. CONV) in wheat rhizosphere and bulk soil. Thirteen phyla were observed, and the most abundant were Proteobacteria (39.6%), Actinobacteria (19.1%) and Acidobacteria (14.9%). Soil bacterial α-diversity increased under CONS relative to CONV management. However, whereas the relative abundances of Bacteroidetes and Firmicutes were greater under CONS than CONV management, the reverse was observed for Acidobacteria and Gemmatimonadetes. Proteobacteria were also more abundant under CONS than CONV management, but only in bulk soil. The community structures of the bacterial communities were in agreement with the differences in relative abundances. These differences were consistent with the ecological classification of soil bacteria as copiotrophic or oligotrophic. Therefore, CONS management systems altered the soil bacterial community profiles and increased the productivity of these soils.

The rhizosphere microbiota contributes immensely to nutrient sequestration, productivity and plant growth. Several studies have suggested that environmental factors and high nutrient composition of plant’s rhizosphere influence the structural diversity of proximal microorganisms. To verify this assertion, we compare the functional diversity of bacteria in maize rhizosphere and bulk soils using shotgun metagenomics and assess the influence of measured environmental variables on bacterial diversity. Our study showed that the bacterial community associated with each sampling site was distinct, with high community members shared among the samples. The bacterial community was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes and Verrucomicrobia. In comparison, genera such as Gemmatimonas, Streptomyces, Conexibacter, Burkholderia, Bacillus, Gemmata, Mesorhizobium, Pseudomonas and Micromonospora were significantly (p ≤ 0.05) high in the rhizosphere soils compared to bulk soils. Diversity indices showed that the bacterial composition was significantly different across the sites. The forward selection of environmental factors predicted N-NO3 (p = 0.019) as the most influential factor controlling the variation in the bacterial community structure, while other factors such as pH (p = 1.00) and sulfate (p = 0.50) contributed insignificantly to the community structure of bacteria. Functional assessment of the sampling sites, considering important pathways viz. nitrogen metabolism, phosphorus metabolism, stress responses, and iron acquisition and metabolism could be represented as Ls &gt, Rs &gt, Rc &gt, Lc. This revealed that functional hits are higher in the rhizosphere soil than their controls. Taken together, inference from this study shows that the sampling sites are hotspots for biotechnologically important microorganisms.

Highlights • Subsolid nodules have higher microbiome diversity compared with solid nodules • Microbiome composition of Subsolid nodules is distinct from that of solid nodules • Microbial signatures show robust performance to predict lung adenocarcinoma or subsolid nodules • Some lung microbial species are associated with clinical characteristics, Objectives Increasing evidence indicates that microbiota dysbiosis in the human body may play vital roles in carcinogenesis. However, the relationship between microbiome and lung cancer remains unclear. In this study, we aimed to characterize the microbiome in early stage of lung adenocarcinoma (LUAD), which presented as subsolid nodules (SSN) or solid nodules (SN). Materials and Methods We performed 16S rRNA sequencing of 35 pairs (10 SSN and 25 SN) of LUAD tumor tissues and paired adjacent normal tissues. Machine learning was used to identify microbial signatures and construct predictive models. Results SSN has higher microbiome richness and diversity compared with SN (richness p = 0.017, Shannon index p = 0.17), and the microbiome composition of SSN is distinct from that of SN (Bray-Curtis p = 0.013, unweighted unifrac p = 0.001). Phylum Chloroflexi (p = 0.009), Gemmatimonadetes (p = 0.018) and genus including Cloacibacterium (p = 0.003), Subdoligranulum (p = 0.002), and Mycobacterium (p = 0.034) were significantly increased in SSN. Tumor and normal tissues had similar richness and diversity, as well as overall microbiome composition. Probiotics with anti-cancer potential, like Lactobacillus, showed elevated levels in normal tissues (p = 0.018). A random forest model with 20 genera-based biomarkers achieved high accuracy for LUAD prediction (area under curve, AUC = 0.879). Meanwhile, a five genera-based signature can accurately discriminate SSN between SN (AUC = 0.950). Cross-validation of these two models also showed high predictive performance (LUAD AUC = 0.813, SSN AUC = 0.933). Conclusions This study demonstrates, for the first time, the tumor bacterial microbiome composition of LUAD manifested as SSN is distinct from that presented as SN, which adds new knowledge to SSN in the perspective of microbiome. Furthermore, microbiome signatures showed good performance to predict LUAD or SSN.

Saline water irrigation can change soil environment, which thereby influence soil microbial process. Based on a field experiment, the shifts in soil microbial metabolic activities and community structures under five irrigation salinities were studied using Biolog and metagenomic methods in this study. The results demonstrated that microbial metabolic activities were greatly restrained in saline water irrigated soils, as average well color development (AWCD) reduced under all saline water irrigation treatments. Although no significant difference in carbon substrate utilization of all six categories was observed among Mild, Medium, High and Severe treatments, the consumption of sole carbon source was significantly varied. Especially, asparagine, galacturonic, putrescine and 4-benzoic acid played a decisive role in dominating the differences. Soil bacterial richness and diversity increased with irrigation salinity while the number of bacterial phyla decreased. Three significantly increased (Proteobacteria, Actinobacteria and Chloroflexi), two decreased (Planctomycetes, Bacteroidetes) and two irresponsive (Gemmatimonadetes and Acidobacteria) phyla were observed as the dominant groups in saline water irrigated soils. The results presented here could improve the understanding of the soil biological process under saline circumstance.

Marine sponges host stable and species-specific microbial symbionts that are thought to be acquired and maintained by the host through a combination of vertical transmission and filtration from the surrounding seawater. To assess whether the microbial symbionts also actively contribute to the establishment of these symbioses, we performed in situ experiments on Orpheus Island, Great Barrier Reef, to quantify the chemotactic responses of natural populations of seawater microorganisms towards cellular extracts of the reef sponge Rhopaloeides odorabile. Flow cytometry analysis revealed significant levels of microbial chemotaxis towards R. odorabile extracts and 16S rRNA gene amplicon sequencing showed enrichment of 'sponge-specific' microbial phylotypes, including a cluster within the Gemmatimonadetes and another within the Actinobacteria. These findings infer a potential mechanism for how sponges can acquire bacterial symbionts from the surrounding environment and suggest an active role of the symbionts in finding their host.

Next Generation Sequencing (NGS) is increasingly affordable and easier to perform. However, standard protocols prior to the sequencing step are only available for few selected sample types. Here we investigated the impact of DNA extraction methods on the consistency of NGS results. Four commercial DNA extraction kits (QIAamp DNA Mini Kit, QIAamp DNA Stool Mini Kit, MO BIO Power Water Kit, and MO BIO Power Soil DNA Isolation Kit) were used on sample sources including lake water and wastewater, and sample types including planktonic and biofilm bacteria communities. Sampling locations included a lake water reservoir, a trickling filter, and a moving bed biofilm reactor (MBBR). Unique genera such as Gemmatimonadetes, Elusimicrobia, and Latescibacteria were found in multiple samples. The Stool Mini Kit was least efficient in terms of diversity in sampling results with freshwater lake samples, and surprisingly the Power Water Kit was the least efficient across all sample types examined. Detailed NGS beta diversity comparisons indicated that the Mini Kit and PowerSoil Kit are best suited for studies that extract DNA from a variety of water and wastewater samples. We ultimately recommend application of Mini Kit or PowerSoil Kit as an improvement to NGS protocols for these sampling environments. These results are a step toward achieving accurate comparability of complex samples from water and wastewater environments by applying a single DNA extraction method, further streamlining future investigations.