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Microbial fuel cells (MFCs) are capable of removing tetracycline in soils, in which the degradation efficiency of tetracycline is hindered by its strong adsorption capacity. Phosphate was chosen as a competitor for tetracycline adsorption to improve its removal rate in soil MFCs. The results showed that 42-50% of tetracycline was degraded within 7 days, which was 42-67% higher than open-circuit treatments. Compared with closed-circuit treatments without phosphate addition, the removal efficiencies of tetracycline after phosphate addition increased by 19-25% on day 51, and accumulated charge outputs were enhanced by 31-52%, while the abundance of antibiotic resistance genes decreased by 19-27%. Like Geobacter, the abundance of Desulfurispora and Anaeroomyxobacter in the anode showed similar tendencies with current densities, suggesting their dominant roles in bioelectricity generation. Gemmatimonadetes bacterium SCN 70-22, Azohydromonas australica, Steroidobacter denitrificans and Gemmatirosa kalamazoonesis were found to be potential electrotrophic microbes in the cathode. The expressed flavoprotein 2,3-oxidoreductase, quinol oxidase and fumarate reductase might have promoted the transfer efficiency of electrons from cathodes to cells, which finally accelerated the biodegradation rate of tetracycline in addition to the polyphenol oxidase. This study provides an insight into functional enzyme genes in the soil microbial electrochemical remediation.

The water and sediments of urban rivers are spatially heterogeneous because of the influence of environmental and anthropogenic factors. However, the spatial and functional diversity of bacterial communities in urban river sediments are unclear. We investigated the spatial distribution of microbial compositions in sediments in Qingdao section of the Dagu River, and the effects of sediment physiochemical properties on the variation were explored. Among the seven heavy metals analyzed, only the average concentration of Cd significantly exceeded the safety limit for sediments. The detailed composition and spatial distribution of bacterial communities fluctuated substantially between sites along the river. Bacterial datasets were separated into three clusters according to the environmental characteristics of sampling areas (the urbanized, scenic, and intertidal zones). For the urbanized zone, Acidobacteria, Firmicutes, Gemmatimonadetes, Bacteroidetes, and Gammaproteobacteria were significantly enriched, implying the effects of human activity. In the intertidal zone, Alphaproteobacteria and Deltaproteobacteria were significantly enriched, which are associated with S redox processes, as in the marine environment. Variation partitioning analysis showed that the amount of variation independently explained by variables of Na, Al, total S and Zn was largest, followed by sediment nutrients, while heavy metals and pH explained independently 13% and 9% of the variance, respectively. Overall, microbial structures in the Dagu River exhibited spatial variation and functional diversity as a result of natural and anthropogenic factors. The results will enable the prediction of the changes in urban river ecosystems that maintain their ecological balance and health.

Soil prokaryotes composition and diversity are the key to uncovering the mechanisms that drive variations in soil biogeochemical processes. Soil erosion is a primary factor that affects the spatial distribution of the soil prokaryotic community, but how soil prokaryotes in soil-eroding catena respond to environmental factors related to topography remains largely unclear. In this study, topsoils were sampled from three typical erosion geomorphic units (autonomous, transitional and depositional zones) in 2018 to identify the soil prokaryotic community and interactions among the species on the Chinese Loess Plateau. The alpha-diversity was greater but the beta-diversity was lower in the autonomous and transitional zones than in the depositional zone. Gammaproteobacteria and Bacteroidetes were 73% and 68% lower in the autonomous and transitional zones than in the depositional zone. In addition, Deltaproteobacteria, Acidobacteria, Firmicutes, Actinobacteria, Chloroflexi, Gemmatimonadetes and Nitrospirae were significantly higher in the autonomous and transitional zones. A less clustered network and fewer co-occurrences within the prokaryotic community and functional groups of processes were found in the depositional zone than in the autonomous and transitional zones. The alpha-diversity index was significantly negatively correlated with clay particles, soil water content, soil organic carbon (SOC), and ratio of SOC and nitrogen (C/N) but positively correlated with total nitrogen (TN). The higher relative abundances of copiotrophic groups (including Gammaproteobacteria, Bacteroidetes, etc.) in the depositional zone was mainly due to the increased SOC caused by the deposition of SOC-rich clay. Reassembly of the soil physico-chemistry characteristics among the topographic units significantly altered the soil prokaryotic community along the soil-eroding catena.

Microbial residues play a significant role in the formation of soil organic matter (SOM), but it is not clear how microbial traits influence residue accrual and SOM persistence. By pairing microbial biomarker and genomics approaches, we tested whether microbial life history strategies and residue accrual differed between primary (~70-year-old) and secondary (~30-year-old) subtropical forests. We found that microbial residue concentrations were significantly higher in secondary than primary forests, and strongly associated with several abundant microbial taxa (Ascomycota, Proteobacteria, Gemmatimonadetes). Microbial communities inhabiting resource-rich secondary forests were also associated with high growth yields and soil organic carbon (SOC) accrual (through residue retention), while nutrient-limited primary forests were dominated by microorganisms employing resource-acquisition strategies. We therefore suggest microbial life history traits can be used to link microbial community composition and metabolic processes with the turnover and transformation of SOC.

Soil microbes play an important role in pollutant remediation and nutrient cycling in urban green spaces. However, how microbial composition and diversity are affected by environmental factors is poorly understood. Here, we compared soil microbial communities in 11 urban parks, constructed at different times (10, ∼30 and >100 years ago) or existing in their natural state. The dominant phyla in the samples were Proteobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, and Planctomycetes. The relative abundance of some phyla showed significant differences between natural forest parks and urban parks. Park construction over a period of time led to significant differences in microbial community structure, which was also significantly correlated with soil pH, moisture, total nitrogen, total carbon, and soil bulk density. Bacterial diversity was significantly positively correlated with pH, and species diversity was not significantly different in each successive park age category. Co-occurrence network analysis revealed that microbial guilds in urban soils were well correlated. Abundant soil microbes in natural forests and hundred-year-old parks had fewer interactions, while abundant bacteria in ten-year-old and thirty-year-old park soils had more interactions. Our results indicate the influence of urban park ages on soil microbial communities, which is important for understanding the effect of urbanization on soil microbes.

To restore highly degraded soil with severe arsenic (As) contamination, effective mitigation of As mobility and bioavailability is considered as the primary step. In this study, the capability of an air-stabilized nano zero-valent iron (A-nZVI) to decrease soil As solubility and leachability was investigated. Further, the effect of A-nZVI on recovery of soil biological function was analyzed by measuring changes in dehydrogenase activity, bacterial community and development of two pioneering plant species. Results showed that A-nZVI exhibited a prominent sorption capacity for both arsenite and arsenate (92.4 and 44.1 mg g−1). With A-nZVI application at ≥0.2%, 44.2–74.7% decline in soil As solubility was achieved in neutral water extraction, while consistently higher As extractability was determined with synthetic precipitation leaching procedure (SPLP, pH 4.2). Compared to adjacent forest soil (F-CK), microbial community of the tested soil was featured by 66% lower abundance of Actinobacteria while an elevated richness of Gemmatimonadetes, both of which showed apparent shift toward F-CK with A-nZVI. 0.2% A-nZVI was most effective in promoting dehydrogenase activity and ryegrass growth. Further, by two-dimensional mapping with the Zr-oxide diffusive gradients in thin films (DGT), averaged DGT-As in rhizosphere of alfalfa (a green manure species) decreased by 47.1% with 0.2% A-nZVI. These results highlight that A-nZVI is critically essential for fixation of soil labile As and thus provides a favorable starting point for recovery of soil health.

This work aimed to evaluate three different strategies for rearing L. vannamei in a biofloc system: heterotrophic, chemoautotrophic and a mature biofloc system relative to the effects of water quality, water bacterial community, biofloc composition and yield. To accomplish this, a study lasting 35 days was conducted with juvenile (3.46 g) shrimps stocked in twelve 300 L tanks at a stocking density of 350 shrimp m3. For heterotrophic treatment, water received molasses as a carbon source. For chemoautotrophic treatment, ammonium and nitrite salts were added to the water. The mature treatment was created by adding a significant amount of water containing mature biofloc from another established biofloc technology (BFT) system. In both mature and chemoautotrophic treatments, the nitrification process could maintain toxic nitrogen compounds (ammonia and nitrite) at low levels without the addition of carbohydrates. In contrast, the heterotrophic system had peaks of ammonia and nitrite during the rearing cycle. The heterotrophic system also had a significantly higher value of volatile solids and total suspended solids compared to the other treatments. Analysis of the biofloc system revealed a relatively high proportion of protein, but the proportion of protein in the heterotrophic system was higher. Chemoautotrophic and mature treatments maintained the water quality at a constant level, especially nitrogen removal. Metagenomic analysis showed the microbial community associated with the biofloc system to be represented by 10 phyla. In all treatments, the five most abundant phyla were the following: Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, and Gemmatimonadetes. Shrimp performance demonstrated that heterotrophic, mature and chemoautotrophic systems are suitable approaches for shrimp rearing in BFT.

The effects of the seasonal groundwater level fluctuations on the redox species in groundwater and the microbial communities in aquifer media were investigated at a typical riverbank filtration (RBF) site in northeast China. A total of 50 groundwater samples were collected to illustrate the variations of oxidation-reduction potential (ORP), dissolved oxygen (DO) and redox species such as iron (Fe2+), manganese (Mn2+), ammonium (NH4+), and nitrate (NO3−) during a whole hydrological year. This study observed that the groundwater dynamics fluctuate seasonally with the amplitude of up to 1.0 m, which is mainly related to the hydrological processes of the Songhua river. The groundwater was oxic with an average DO value of 3.6 mg/L and 3.2 mg/L in the two seasons. The ORP measurements showed that the groundwater was mostly under reducing conditions, with the seasonal variations of ORP being concurrent with the water level fluctuation. As electron acceptors, the average values of Fe2+ and Mn2+ were 6.3 mg/L and 6.8 mg/L, and 1.2 mg/L and 1.4 mg/L in wet and dry seasons, respectively. The O2 entrapment induced by the seasonal groundwater level fluctuation facilitates the interaction among O2, Fe2+ and Mn2+ for biotransformation. Moreover, the reductive dissolution of iron and manganese oxides might be major mechanisms for Fe2+ and Mn2+ release under reductive conditions. The average content of NH4+ was 1.5 mg/L and 1.2 mg/L in two seasons, respectively, and NO3− was lower than 0.1 mg/L. The seasonal variation of NH4+ and NO3− in groundwater is mainly related to the periodic application of nitrogen fertilizer in agriculture. The spatiotemporal of microbial communities was significantly different between the two seasons, and Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, Nitrospirae, Gemmatimonadetes, Bacteroidetes, and Verrucomicrobia were the nine main phyla. pH, DO, EC, NO2−, and Fe2+ were the major factors correlating the microbial community in the wet season, while pH, NO2−, NH4+, TH, COD, and SO42− were the critical parameters in the dry season according to RDA results. These results may be valuable to gain insight into the temporal variation of the redox species due to groundwater seasonal fluctuation and to identify the correlation between the groundwater and microbial communities in the redox-dynamic zone.

Denitrification and anammox are the main pathways of N loss in wet habitats while their relative contribution to N2 production and underlying microbial mechanisms across marine-terrestrial ecotone remain unclear. Here we investigated the rates of anammox and denitrification, and the distribution patterns of anammox bacteria and nosZ clade I and II denitrifiers across coastal tidal flat to inland paddy soils. Results showed that denitrification dominated the N2 production over anammox in all samples, accounting for 87.1%–100% of total N2 production. Coincident with the rate, the abundance of nosZ clade I and II genes were 1–2 orders of magnitude higher than those of hzsB gene. The community of anammox bacteria was mainly driven by salinity while nosZ clade I and II denitrifiers communities were mainly determined by both salinity and pH. Alphaproteobacteria dominated in the nosZ clade I community in all samples while Betaproteobacteria and Gammaproteobacteria were mainly present in low salinity wetland and paddy soils. The nosZ clade II community was composed of more phyla, in which Bacteoidetes and Chloroflexi were ubiquitous while Gemmatimonadetes was present only in low salinity wetland and paddy soils. These findings have direct implications for explicitly incorporating both nosZ clade I and II into future N loss estimation and N2O mitigation in marine-terrestrial ecotone.

The herbicides imazethapyr and flumyzin have been recommended for controlling weeds, mainly in soybean fields. However, it is unclear the effect of these herbicides on soil microbial communities. In this study, we assessed the responses of bacterial community to the application of imazethapyr and flumyzin in soil. Soil samples were incubated with the application of the herbicides imazethapyr, flumyzin, and their mixture, and analyzed at 0, 15, 30, and 60 days. The abundance of specific microbial phyla changed as a response of the herbicide application with a significant decrease of Acidobacteria, Verrucomicrobia, Elusimicrobia, and Planctomycetes, and an increase of Gemmatimonadetes, Bacteroidetes, Firmicutes, and Proteobacteria. The principal component analysis clustered the samples according to the time of incubation and the microbial diversity increased on the 15th day with a trend to decrease at 30 and 60 days. The evaluation of potential functions has shown the core functions represented by chemoheterotrophy (35.1%), followed by aerobic chemoheterotrophy (32.8%), nitrification (6.2%), ammonia oxidation (6.2%), and aromatic compound degradation (4.4%). Our data showed an increase of microbial groups that have the potential to metabolize the chemical compounds, such as the genera Bryobacter, Gaiella, and Flavobacterium, which increased significantly in abundance and can be explored for future biotechnological use. Finally, this study shows that the application of the herbicides in soil affects the microbial profile with the potential to affect functions mediated by microbial communities, and this effect is related to groups with the potential to degrade the compound.

Soybean (Glycine max L.) is among the most economically important legumes that provide more than 1/4 of food (for man) and animal feed. However, its yield is comparatively low, most especially under drought stress. The aim of this study therefore was to assess the ability of Rhizobium spp. and mycorrhizal fungi to enhance the yield, seed size and fatty acid content of soybean grown under semi-arid environment. Rhizobium sp. strain R1 was found to possess nitrogen-fixing gene coniferyl aldehyde dehydrogenase function while Rhizobium cellulosilyticum strain R3 was found to have nitrogen-fixing genes cysteine desulfurase SufS and cysteine desulfurase IscS activity. Soybean (Glycine max L) seeds inoculated with Rhizobium spp. and mycorrhizal fungi were cultivated in soil exposed to drought stress. Rhizobium spp. inoculation and mycorrhization alleviate drought stress and increase yield, size and fat content of soybean seeds. This increase in the aboveground parameters was accompanied with an increase in belowground mycorrhizal spore number, percentage root mycorrhization and aboveground shoot relative water content (RWC) in the dually inoculated (R1 + R3MY) soybean plants. In particular, the dually inoculated (R1 + R3MY) soybean plants revealed 34.3 g fresh weight, 15.1 g dry weight and soybean plants singly inoculated with Rhizobium sp. strain R1 (R1) produced more large seeds with 12.03 g dry weight. The non-inoculated (control) seeds contained a higher percentage of moisture content compared to the microbially amended seeds while seeds co-inoculated with Rhizobium cellulosilyticum strain R3 and mycorrhizal consortium revealed the highest percent (8.4 %) of fat. Several fatty acids that are of significant health benefits to humans were observed in the soybean seeds. In order to gain insights into the bacterial communities of rhizospheric soil collected at different stages of soybean growth, class-based Heat-map analysis was performed on the Miseq sequenced data. The core bacteria that were found in the rhizospheric soil were Verrumicrobia, Proteobacteria, Gemmatimonadetes, Firmicutes, Cyanobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Acidobacteria, Planctomycetes, Deinococcus thermus and Nitrospira suggesting that the rhizobia and fungi used in this study can also improve soil microbial diversity.

Soil microbes play an important role in nutrient cycling in agricultural soils and can be influenced by tillage. Conservation tillage aims to reduce energy inputs and conserve soil and water by decreasing disturbance of soil and returning a portion of crop residue. The response of the soil microbial community to conservation tillage is complex and quantitative analysis is largely absent regarding how tillage and depth, combined with soil properties, affect soil microbial diversity and community composition. Here, the diversity and composition of the soil bacterial community and its relationship with soil properties were explored by high-throughput sequencing technology and Structural Equation Modeling (SEM) at two soil depths (0–5 cm and 15–20 cm) under conventional tillage and no tillage with residue retention. No tillage significantly increased alpha diversity (Chao 1 and Shannon) at 0-5 cm and altered the composition of the bacterial community, coinciding with changes in physical-chemical properties. Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the most abundant phyla across all samples. Alpha diversity was significantly correlated with soil bulk density (BD) and pH. The SEM showed that tillage and depth explained 86% of the bacterial diversity and 84% of the composition. In addition, tillage and depth had indirect effects on bacterial diversity and composition by affecting soil BD, pH and soil organic carbon. Results indicate that the soil bacterial community is altered by conservation tillage, especially in the topsoil, and highlight the importance of soil physical-chemical properties in shaping the diversity and composition of the soil bacterial community. Our findings contribute to a broad understanding of tillage disturbance and differentiated effects in the soil profile for the bacterial community.

For typical copper producing provinces of Heilongjiang, Henan, Inner Mongolia, Jiangxi, Shandong, Tibet, and Yunnan in China, 90 % of sampling sites were heavily polluted with multiple heavy metals. Soil heterogeneity and mutual interference of multimetals are obstacles to explore bacterial resistance pathways in contaminated field soils. Through analyses of contamination indices and bioindicators, combined with multivariate statistical models, the antioxidant enzyme activity, urease-induced precipitation of heavy metals, excretion of extracellular polymeric substances (EPS) were attributed to different types of heavy metals. Furthermore, through redundancy analysis combined with phylogenetic analysis of metal-resistant bacteria, we identified that Verrucomicrobia, Acidobacteria, and Planctomycetes secreted EPS-polysaccharides and EPS-proteins to detoxify Cr, a metal with lower concentrations and lower ecological risk as compared to other metals. The pathway was innovatively differentiated from the multimetal resistance pathways in urease and/or catalase-producing bacteria such as Proteobacteria, Firmicutes, BRC1, Bacteroidetes, Dadabacteria, Entotheonellaeota, Nitrospirae, and Gemmatimonadetes using field studies and high-throughput sequencing. Moreover, these metal-resistant bacteria were linked to C/N cycling processes of urea hydrolysis, nitrification, denitrification, EPS production, and calcite precipitation. It will provide new insight into soil bacterial resistance to multimetals in field studies.

Polymer modifiers are widely used in the remediation of cadmium-contaminated soil. However, little is known about how polymer modifiers affect soil bacterial communities. The purpose of this study was to measure the effects of polymer modifiers (polyacrylate polymer and organic polymer) on the composition and network structure of bacterial communities in cadmium-contaminated soils combined with phloem girdling of cotton. The results showed that polyacrylate polymer increased soil urease, sucrase, and alkaline phosphatase activities (P Mn oxides-bound Cd), Org-Cd (organic Cd), and Res-Cd (residuals Cd) concentrations. Polyacrylate polymer increased the relative abundances of Proteobacteria, Gemmatimonadetes, and Chloroflexi (P

Gemmatimonas phototrophica is, so far, the only described phototrophic species of the bacterial phylum Gemmatimonadetes. Its cells contain a unique type of photosynthetic complex with the reaction center surrounded by a double ring antenna, however they can also grow in the dark using organic carbon substrates. Its photosynthesis genes were received via horizontal gene transfer from Proteobacteria. This raises two questions; how the horizontally transferred photosynthesis apparatus has integrated into the cellular machinery, and how much light-derived energy actually contributes to the cellular metabolism? To address these points, the photosynthetic reactions were studied on several levels, from photophysics of the reaction center to cellular growth. Flash photolysis measurements and bacteriochlorophyll fluorescence kinetic measurements documented the presence of fully functional type-2 reaction centers with a large light harvesting antenna. When illuminated, the bacterial cells reduced their respiration rate by 58 ± 5%, revealing that oxidative phosphorylation was replaced by photophosphorylation. Moreover, illumination also more than doubled the assimilation rates of glucose, a sugar that is mostly used for respiration. Finally, light increased the growth rates of Gemmatimonas phototrophica colonies on agar plates. All the presented data provide evidence that photosynthetic complexes are fully integrated into cellular metabolism of Gemmatimonas phototrophica, and are able to provide a substantial amount of energy for its metabolism and growth.

Yellow River Delta undergoes intensive conversion from natural wetland to agricultural fields and artificial woodland. In this study, we analysed how the conversion affects bacterial community diversity and composition by Illumina Miseq sequencing combined with functional prediction. Compared to natural wetland, arable land and woodland were featured with higher soil organic matter, total nitrogen and bacterial diversity, but lower electrical conductivity. The bacteria Gemmatimonadetes related to soil organic matter and total nitrogen, was enriched in arable land, while salt-resistant bacteria (e.g. phylum Chloroflexi and its class Ardenticatenia) were abundant in natural wetland. Moreover, the relative abundances of the nitrifying bacteria Nitrospira and Nitrosospira were significantly higher in arable land and woodland than in natural wetland, suggesting that land use changes significantly affect the bacterial processes involved in nitrogen cycling. Redundancy analysis (RDA) showed that the differences in bacterial community were attributed to soil nutrient-related properties (i.e., total nitrogen and soil organic matter), soil salinity (i.e., electrical conductivity), and heavy metals (i.e. Cu and Cr). PICRUSt results revealed that land use conversion from natural wetland to arable land increased soil functions, e.g., biosynthesis process and oxidative phosphorylation. The data help us elucidate how land use changes affect terrestrial ecosystem function, and advise local farmers to apply the suitable land-use strategies and keep agricultural sustainable development.

Native soil amendment has been widely used to stabilize mine tailings and speed up the development of soil biogeochemical functions before revegetation; however, it remains poorly understood about the response of microbial communities to ecological restoration of mine tailings with soil-covered strategy. In this study, microbial communities along a 60-cm profile were investigated in mine tailings during ecological restoration of two revegetation strategies (directly revegetation and native soil covered) with different plant species. The mine tailings were covered by native soils as thick as 40 cm for more than 10 years, and the total nitrogen, total organic carbon, water content, and heavy metal (Fe, Cu, and Zn) contents in the 0-40 cm intervals of profiles were changed. In addition, increased microbial diversity and changed microbial community structure were also found in the 10-40 cm intervals of profiles in soil-covered area. Soil-covered strategy rather than plant species and soil depth was the main factor influencing the bacterial community, which explained the largest portion (29.96%) of the observed variation. Compared directly to revegetation, soil-covered strategy exhibited the higher relative abundance of Acidobacteria and Deltaproteobacteria and the lower relative abundance of Bacteroidetes, Gemmatimonadetes, Betaproteobacteria, and Gammaproteobacteria. PICRUSt analysis further demonstrated that soil-covered caused energy metabolic functional changes in carbon, nitrogen, and sulfur metabolism. Given all these, the soil-covered strategy may be used to fast-track the establishment of native microbial communities and is conducive to the rehabilitation of biogeochemical processes for establishing native plant species.

This study compared rhizobacterial communities in pepper greenhouses under a paddy-upland (rice-pepper) rotational system (PURS) and a monoculture repeated cropping system (RCS) and examined adverse effects of high salinity on soil properties. The following soil properties were analyzed: electrical conductivity (EC), pH, concentration of four cations (Na, Ca, Mg, and K), total nitrogen, and organic matter content. Rhizobacterial communities were analyzed using culture-based and culture-independent (pyrosequencing) methods. In addition, all culturable bacteria isolated from each soil sample were tested for traits related to plant growth promotion. The EC of rhizospheric soils was 5.32-5.54 dS/m for the RCS and 2.05-2.19 dS/m for the PURS. The culture-based method indicated that the bacterial communities and bacterial characteristics were significantly more diverse in the PURS soil than in the RCS soil. The pyrosequencing data also indicated that the richness and diversity of bacterial communities were greater in the PURS soil. Proteobacteria was the most abundant phylum in soil samples under both cropping systems. However, Firmicutes and Gemmatimonadetes were more prevalent in the RCS soil, while the PURS soil contained a greater number of Chloroflexi. Spearman's correlation coefficients showed that soil EC was significantly positively correlated with the abundance of Firmicutes and Gemmatimonadetes and negatively correlated with the abundance of Acidobacteria, Chloroflexi, and Deltaproteobacteria. This is the first study on the rhizobacterial communities in pepper greenhouses under two different cropping systems using both culture- and pyrosequencing-based methods.

The redistribution of soil and associated organic matter across landscape represents a major perturbation to the carbon cycle because the established colluvial soils change the levels of C mineralization and sequestration. In this study, two profiles of a colluvial soil 4 m deep were analyzed to test whether its two layers produced by erosion differ from the organic layer of the original soil and if the microbial characteristics correspond to the soil properties. The structure of microbial communities was assessed by both quantitative PCR and Illumina amplicon sequencing. Microbial activities were determined by hydrolytical enzymes. The bacterial community structure was correlated with vertical gradients of soil chemical properties. The dominating bacterial phyla were the same along the whole profile but their relative abundance changed. The upper horizon determined by tillage and reaching to approx. 75 cm had highest values of dissolved organic carbon, P and K and was characterized by Proteobacteria and Bacteroidetes . Also, the activities of hydrolytical enzymes occurred mostly there. The second horizon of deposited soil reaching to approx. 250 cm was characterized by Acidobacteria and Gemmatimonadetes . The lowest horizon of buried Chernozem was characterized by increased soil organic carbon, manganese, iron and sulfate and characterized by Nitrospirae and Rubrobacteria . The community analysis indicated that chemolithotrophic processes might be important in these buried horizons so the decomposition may be slower and residence times for these deep carbon pools longer than in the original upper horizons. In these colluvial systems, erosion could lead to soil organic C stabilization.

The evolution and diversification of different types of photosynthetic reaction centers (RCs) remains an important unresolved problem. We report here novel sequence features of the core proteins from Type I RCs (RC-I) and Type II RCs (RC-II) whose analyses provide important insights into the evolution of the RCs. The sequence alignments of the RC-I core proteins contain two conserved inserts or deletions (indels), a 3 amino acid (aa) indel that is uniquely found in all RC-I homologs from Cyanobacteria (both PsaA and PsaB) and a 1 aa indel that is specifically shared by the Chlorobi and Acidobacteria homologs. Ancestral sequence reconstruction provides evidence that the RC-I core protein from Heliobacteriaceae (PshA), lacking these indels, is most closely related to the ancestral RC-I protein. Thus, the identified 3 aa and 1 aa indels in the RC-I protein sequences must have been deletions, which occurred, respectively, in an ancestor of the modern Cyanobacteria containing a homodimeric form of RC-I and in a common ancestor of the RC-I core protein from Chlorobi and Acidobacteria. We also report a conserved 1 aa indel in the RC-II protein sequences that is commonly shared by all homologs from Cyanobacteria but not found in the homologs from Chloroflexi, Proteobacteria and Gemmatimonadetes. Ancestral sequence reconstruction provides evidence that the RC-II subunits lacking this indel are more similar to the ancestral RC-II protein. The results of flexible structural alignments of the indel-containing region of the RC-II protein with the homologous region in the RC-I core protein, which shares structural similarity with the RC-II homologs, support the view that the 1 aa indel present in the RC-II homologs from Cyanobacteria is a deletion, which was not present in the ancestral form of the RC-II protein. Our analyses of the conserved indels found in the RC-I and RC-II proteins, thus, support the view that the earliest photosynthetic lineages with living descendants likely contained only a single RC (RC-I or RC-II), and the presence of both RC-I and RC-II in a linked state, as found in the modern Cyanobacteria, is a derivation from these earlier phototrophs.

Anoxygenic phototrophs represent an environmentally important and phylogenetically diverse group of organisms. They harvest light using bacteriochlorophyll-containing reaction centers. Recently, a novel phototrophic bacterium, Gemmatimonas phototrophica , belonging to a rarely studied phylum, Gemmatimonadetes , was isolated from a freshwater lake in the Gobi Desert. To obtain more information about the environmental distribution of phototrophic Gemmatimonadetes , we collected microbial samples from the water column, upper sediment, and deeper anoxic sediment of Lake Taihu, China. MiSeq sequencing of the 16S rRNA, pufM , and bchY genes was carried out to assess the diversity of local phototrophic communities. In addition, we designed new degenerate primers of aerobic cyclase gene acsF , which serves as a convenient marker for both phototrophic Gemmatimonadetes and phototrophic Proteobacteria . Our results showed that most of the phototrophic species in Lake Taihu belong to Alpha - and Betaproteobacteria . Sequences of green sulfur and green nonsulfur bacteria (phototrophic Chlorobi and Chloroflexi , respectively) were found in the sediment. Using the newly designed primers, we identified a diverse community of phototrophic Gemmatimonadetes forming 30 operational taxonomic units. These species represented 10.5 and 17.3% of the acsF reads in the upper semiaerobic sediment and anoxic sediment, whereas their abundance in the water column was IMPORTANCE Photosynthesis is one of the most fundamental biological processes on Earth. Recently, the presence of photosynthetic reaction centers has been reported from a rarely studied bacterial phylum, Gemmatimonadetes , but almost nothing is known about the diversity and environmental distribution of these organisms. The newly designed acsF primers were used to identify phototrophic Gemmatimonadetes from planktonic and sediment samples collected in Lake Taihu, China. The Gemmatimonadetes sequences were found mostly in the upper sediments, documenting the preference of Gemmatimonadetes for semiaerobic conditions. Our results also show that the phototrophic Gemmatimonadetes present in Lake Taihu were relatively diverse, encompassing 30 operational taxonomic units.

Few molecular studies have shown that the number of bacterial species in implant-associated infection may have been underestimated. To determine the actual microbial diversity in implant-associated infection, a high-throughput sequencing method was adopted to sequence the DNAs extracted from the tissues of infected and uninfected patients. Principal component analysis (PCA) and β diversity showed an obvious divergence of infected and uninfected groups, and that the overgrowth of Proteobacteria (80.87%), Firmicutes (13.41%) in the positive deep infection group (P.d, via biopsy) and Proteobacteria (91.68%) in the positive surface infection group (P.s, via swabs) might be the causative factors in implant-associated infection. Moreover, Venn results indicated that a mean of 330 common operational taxonomic units (OTUs) was obtained in all groups, of which 113, 109, 45, 20, 13 and 12 OTUs belonging to Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes and Chloroflexi were identified. In conclusion, many traditional "pathogenic bacteria" were identified as the common bacteria in operation sites, and the disruption of their complex interaction caused infection; therefore, further work is need to illustrate the aetiology of implant-associated infection using in-depth systems-level analyses.

Wheat and maize are increasingly used as alternative crops to sunflower monocultures that dominate the Hetao Irrigation District in China. Shifts from sunflower monocultures to alternate cropping systems may have significant effects on below-ground microbial communities which control nutrient cycling and influence plant productivity. In this research, rhizosphere bacterial communities were compared among sunflower, wheat and maize cropping systems by 454 pyrosequencing. These cropping systems included 2 years wheat (cultivar Yongliang 4) and maize (cultivar Sidan 19) monoculture, more than 20 years sunflower (cultivar 5009) monoculture, and wheat-sunflower and maize-sunflower rotation. In addition, we investigated rhizosphere bacterial communities of healthy and diseased plants at maturity to determine the relationship between plant health and rotation effect. The results revealed taxonomic information about the overall bacterial community. And significant differences in bacterial community structure were detected among these cropping systems. Eight of the most abundant groups including Proteobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Chloroflexi, Actinobacteria, Planctomycetes and Firmicutes accounted for more than 85% of the sequences in each treatment. The wheat-wheat rhizosphere had the highest proportion of Acidobacteria, Bacteroidetes and the lowest proportion of unclassified bacteria. Wheat-sunflower cropping system showed more abundant Acidobacteria than maize-sunflower and sunflower monoculture, exhibiting some influences of wheat on the succeeding crop. Maize-maize rhizosphere had the highest proportion of γ-Proteobacteria, Pseudomonadales and the lowest proportion of Acidobacteria. Sunflower rotation with wheat and maize could increase the relative abundance of the Acidobacteria while decrease the relative abundance of the unclassified phyla, as was similar with the health plants. This suggests some positive impacts of rotation with wheat and maize on the bacterial communities within a single field. These results demonstrate that different crop rotation systems can have significant effects on rhizosphere microbiomes that potentially alter plant productivities in agricultural systems.

Agricultural management practices impact the bacterial diversity of soil but it is unclear how bacterial communities respond to different nutrient sources. This study examined the impacts of manure and granular urea N additions on the diversity and composition of soil bacterial communities. Bacterial communities in an annual cropping system were examined in the short-term (within season) and medium-term (after three successive annual additions) following manure and urea N applications. Soil samples were collected from an experimental field site in fall 2007 prior to imposition of treatments, and post-planting, mid-season, and post-harvest in 2010 following three successive annual applications. Treatments included: solid pig manure (SPM), solid dairy manure (SDM), granular urea N-fertilizer, and unamended control. Pyrosequencing was used to characterize bacterial communities in soil and the manure added. Psychrobacter was the most abundant genus in both SPM and SDM, however it was not detected in soil. Solid pig manure treatments had greater diversity than urea and control treatments and diversity was greatest at post-harvest in fall than post-planting in spring. In 2010, the relative abundances of many bacterial taxa were affected by treatment and sample season but not their interaction. Where Actinobacteria, Firmicutes, Gemmatimonadetes and Bacteroidetes were significantly different for the urea and manure treatments, Proteobacteria declined in relative abundance over the growing season. Communities of manure and urea treated soils converged with progression of growing season. Redundancy analysis showed SO 4 −2 , NO 3 − and NH 4 + concentrations were significant, explaining 44% of the variation observed in bacterial communities across treatments and sample seasons. In conclusion, bacterial diversity increased with manure treatment and with progression of the growing season, the former being not as a result of introduction of taxa from the manure but likely from nutritional resources provided in the organic amendments.

Sewage sludge and manure are common soil amendments in crop production; however, their impact on the abundance and diversity of the antibiotic resistome in soil remains elusive. In this study, by using high-throughput sequencing and high-throughput quantitative PCR, the patterns of bacterial community and antibiotic resistance genes (ARGs) in a long-term field experiment were investigated to gain insights into these impacts. A total of 130 unique ARGs and 5 mobile genetic elements (MGEs) were detected and the long-term application of sewage sludge and chicken manure significantly increased the abundance and diversity of ARGs in the soil. Genes conferring resistance to beta-lactams, tetracyclines, and multiple drugs were dominant in the samples. Sewage sludge or chicken manure applications caused significant enrichment of 108 unique ARGs and MGEs with a maximum enrichment of up to 3845 folds for mexF. The enrichment of MGEs suggested that the application of sewage sludge or manure may accelerate the dissemination of ARGs in soil through horizontal gene transfer (HGT). Based on the co-occurrence pattern of ARGs subtypes revealed by network analysis, aacC, oprD and mphA-02, were proposed to be potential indicators for quantitative estimation of the co-occurring ARGs subtypes abundance by power functions. The application of sewage sludge and manure resulted in significant increase of bacterial diversity in soil, Proteobacteria, Acidobacteria, Actinobacteria and Chloroflexi were the dominant phyla (>10% in each sample). Five bacterial phyla (Chloroflexi, Planctomycetes, Firmicutes, Gemmatimonadetes and Bacteroidetes) were found to be significantly correlated with the ARGs in soil. Mantel test and variation partitioning analysis (VPA) suggested that bacterial community shifts, rather than MGEs, is the major driver shaping the antibiotic resistome. Additionally, the co-occurrence pattern between ARGs and microbial taxa revealed by network analysis indicated that four bacterial families might be potential hosts of ARGs. These results may shed light on the mechanism underlining the effects of amendments of sewage sludge or manure on the occurrence and dissemination of ARGs in soil. Keywords: Antibiotic resistance genes, Bacterial pathogens, Horizontal gene transfer, Network analysis, Sewage sludge

Rhizosphere soil bacterial communities are crucial to plant growth, health, and stress resistance. In order to detect how bacterial communities associated with the rhizosphere of phylogenetically related plant species vary in terms of composition, function, and diversity, we investigated the rhizosphere bacterial community structure of two perennial shrub species, Caragana jubata and Caragana roborovskyi, under natural field conditions in northwest China and analyzed the influence of soil properties and environmental factors. Eighteen root samples, eight for C. jubata, and ten for C. roborovskyi, along with any adherent soil particles, were collected from multiple sites in northwest China. The rhizosphere soil was washed from the roots, and bacterial communities were analyzed using Illumina MiSeq sequencing of 16S rRNA gene amplicons. Then, α-diversity and β-diversity were calculated using QIIME. Across species, Proteobacteria (29 %), Actinobacteria (15 %), Chloroflexi (10 %), Acidobacteria (10 %), Bacteroidetes (8 %), Firmicutes (8 %), Planctomycetes (7 %), Gemmatimonadetes (4 %), and Verrucomicrobia (3 %) were the most abundant phyla in the rhizosphere of C. jubata and C. roborovskyi. However, principal co-ordinates analysis indicated strong interspecific patterns of bacterial rhizosphere communities. Further, the richness of Proteobacteria, Acidobacteria, Bacteroidetes, Verrucomicrobia, Firmicutes, and Nitrospirae was significantly higher in the rhizosphere of C. jubata compared with C. roborovskyi, while the opposite was found for Actinobacteria and Cyanobacteria. However, the Shannon index showed no significant difference in α-diversity between C. jubata and C. roborovskyi. Distance-based redundancy analysis indicated that soil properties and environmental factors exerted strong influences on the structure of the rhizosphere bacterial community and explained 47 and 46 % of community variances between samples, respectively. Our results showed strong interspecific clustering of the bacterial rhizosphere communities of C. roborovskyi and C. jubata. Altitude explained most of the variation in the composition of bacterial rhizosphere communities of C. roborovskyi and C. jubata, followed by soil pH, water content, organic matter content, total nitrogen content, and mean annual rainfall.

The objective of this study was to access the effect of long-term fertilization and film mulching application on soil properties and bacterial community structure. We used 16S rRNA gene to investigate soil bacterial community composition by high through-put sequencing. The results demonstrated that predominant groups in the bacterial community were: Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi and Cyanobacteria. Long-term fertilization of combined manure and nitrogen application caused significant decrease in soil bacterial diversity and richness compared to non-fertilization control, though manure fertilization alone played a significant role in restoring bacterial diversity. Film mulching and manure fertilization significantly increased the relative abundances of soil bacterial groups mentioned above. Furthermore, film mulching played significant role in shaping the bacterial community structure regardles...

The Arctic Ocean is undergoing a rapid change due to global climate change. Knowledge about bacterial community composition will help us to evaluate their ecological role and predict possible community shifts in future. To this end, we collected 11 sediment samples across the western Arctic Ocean from shelf near to the North Pole, spanning three geographical regions: ice-free Chukchi Shelf, more than 90 % ice-covered Canadian Basin and the partial ice-covered slopes between them. The spatial distribution of bacterial community composition was examined by 16S rRNA gene using Illumina high-throughput sequencing in conjunction with sediment geophysicochemical variables and sampling geographical distance. Overall, Proteobacteria, Acidobacteria, Planctomycetes, Actinobacteria, Chloroflexi, Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospira and Thermomicrobia were the top ten dominant phyla. The bacterial communities from the same region exhibited similar composition pattern, but distinctive in each region. Statistical analysis (linear discriminant analysis effect size) showed Deltaproteobacteria, Gammaproteobacteria and Alphaproteobacteria were the distinct taxa in Chukchi Shelf, Slopes and Canadian Basin, respectively. Correspondingly, Desulfobacterales, Planctomycetales and Rhodospirillales were determined at order level. Canonical correspondence analysis demonstrated bacterial distribution was significantly correlated with sediment geophysicochemical factors and geographical distance. Furthermore, variance partitioning analysis confirmed that the combination of geophysicochemical factors, including sediment nutrients content, grain size, sampling site water depth and ice coverage, contributed more than geographical distance to the spatial distribution of bacterial communities across the western Arctic Ocean. In general, this study offers a snapshot of bacterial community composition under the background in rapidly changing Arctic Ocean.

The goal of this study was to determine the relationships between the structure of the soil microbiome and the agroecological state of soils by the example of natural undisturbed (steppe areas) and anthropogenically disturbed (pastures, croplands, fallows) areas in the territory of northwestern Kazakhstan. The highest abundance of proteobacteria was found in the anthropogenically disturbed of fallows and in undisturbed soils; in other cases, actinobacteria and representatives of the Firmicutes phylum predominated. Different kinds of anthropogenic impacts resulted in the decrease in the portions of bacteria from the Acidobacteria, Gemmatimonadetes, and Firmicutes phyla. In the disturbed soils, the portions of bacteria from the Erysipelothrix, Mycobacterium, Methylibium, Skermanella, Ralstonia, Lactococcus, Bdellovibrio, Candidatus nitrososphaera, Catellatospora, Cellulomonas, Stenotrophomonas, and Steroidobacter genera increased. Bacteria of the Erysipelothrix and Methylibium genera occurred only in the undisturbed soils. The anthropogenically disturbed and undisturbed soils differed significantly in the taxonomic structure of their microbiomes forming two separate clusters, which confirms the efficiency of using the data on the structure of soil microbiomes when assessing the agroecological status of soils.

Fusarium wilt in cucumber results from continuous cropping and is a serious soil-borne fungal disease that threatens cucumber production around the world. The application of a novel fumigation agent based on ammonium bicarbonate to the soil as a strategy for controlling Fusarium wilt and its effects on soil microflora was investigated in a field with serious disease incidence in this study. Overall, the results showed that fumigation effectively controlled cucumber Fusarium wilt disease and significantly increased the total and mean cucumber fruit weight. Real-Time PCR results showed that the total bacterial and fungal numbers in the treatment (LAB) significantly decreased after fumigation and that significantly fewer fungi were observed after harvest (LABOF). The next-generation sequencing of the 16S rRNA and internal transcribed spacer (ITS) genes using MiSeq platform showed that the soil bacterial and fungal community structures in the fumigation treatment were significantly different from the control without fumigation regardless after fumigation or harvest. Compared to the control, higher abundances of Gemmatimonadetes, Verrucomicrobia and Zygomycota, and lower abundance of Ascomycota were observed in the fumigated soils after fumigation and harvest. Furthermore, the abundances of Mortierella and Gp1 were significantly higher. Most importantly, the abundance of Fusarium, which includes the pathogen potentially responsible for cucumber Fusarium wilt disease, was significantly lower in the fumigated soils after harvest. Redundancy analysis showed that the fumigated soils were dominated by Ohtaekwangia, Gp6, and Gp4, which were related to the soil total nitrogen (TN), ammonium nitrogen (NH4–N) and nitrate nitrogen (NO3–N) contents. In addition, Penicillium and Pseudaleuria fungi were dominant in the treatment and control, and the control was dominated by Fusarium. In conclusion, the observed disease suppression due to the novel ecological soil fumigation strategy may be attributed to general suppression resulting from altered soil properties, such as higher soil NH4–N, NO3–N and TON contents, and the alteration of the disturbed soil microflora in a cucumber monoculture system.

Previous studies already demonstrated that biochar addition reduces nitrogen (N) leaching in soil, but little information is available about its effects on N leaching and bacterial community structure under the application of organic N. This study investigated the effects of corn-straw biochar under the application of urea (250 kg N ha−1) in layered soil columns. The PCR-amplified partial 16S rRNA genes in soil were sequenced before and after biochar treatment in order to assess the change of bacterial diversity and community structure utilizing the Illumina technology. With the application of 2% (B2), 4% (B4) and 8% (B8) biochar (mass ratio), the cumulative amount of total leached nitrogen was reduced by 18.8%, 19.5% and 20.2%, respectively (P

Many studies have investigated patterns in the near-surface soil microbial community over large spatial scales. However, less is known about variation in subsurface (15-30 cm of depth) microbial communities. Here we studied depth profiles of microbial communities in high-elevation soils from Tibet. The relative abundance of Acidobacteria, Chloroflexi and Alphaproteobacteria was higher in near-surface layers, while the relative abundance of Actinobacteria, Gemmatimonadetes and Betaproteobacteria was higher in the subsurface samples. The microbial community structure was distinct between the surface and subsurface soil layers, strongly correlating with variation in total carbon (TC) and carbon to nitrogen ratio (C/N). The differences in the microbial community between the layers were about the same as the horizontal differences between sites separated by many kilometers. Overall, we found that TC and C/N were the best predictors for both surface and subsurface microbial community distribution. Exploration of the relative contribution of distance and environmental variables to community composition suggests that the contemporary environment is the primary driver of microbial distribution in this region. Reflecting niche conservatism in evolution, the microbial communities in each soil site and layer tended to be more phylogenetically clustered than expected by chance, and surface soil layer samples were more likely to be clustered than subsurface samples.

Summary Diverse intercropping system has been used to control disease and improve productivity in the field. In this research, the bacterial communities in salt–alkali soils of monoculture and intercropping mulberry and soybean were studied using 454-pyrosequencing of the 16S rDNA gene. The dominant taxonomic groups were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Planctomycetes and Gemmatimonadetes and these were present across all samples. However, the diversity and composition of bacterial communities varied between monoculture and intercropping samples. The estimated bacterial diversity (H') was higher with intercropping soybean than in monoculture soybean, whereas H' showed an opposite pattern in monoculture and intercropping mulberry. Populations of Actinobacteria, Acidobacteria, and Proteobacteria were variable, depending on growth of plants as monoculture or intercropped. Most of Actinobacteria and Chloroflexi were found in intercropping samples, while Acidobacteria and Proteobacteria were present at a higher percentage in monoculture samples. The plant diversity of aboveground and microbial diversity of belowground was linked and soil pH seemed to influence the bacterial community. Finally, the specific plant species was the major factor that determined the bacterial community in the salt–alkali soils.

Plant-associated microorganisms can stimulate plants growth and influence both crops yield and quality by nutrient mobilization and transport. Therefore, rhizosphere microbiome appears to be one of the key determinants of plant health and productivity. The roots of plants have the ability to influence its surrounding microbiology, the rhizosphere microbiome, through the creation of specific chemical niches in the soil mediated by the release of phytochemicals (i.e. root exudates) that depends on several factors, such as plants genotype, soil properties, plant nutritional status, climatic conditions. In the present research, two different crop species, namely barley and tomato, characterized by different strategies for Fe acquisition, have been grown in the RHIZOtest system using either complete or Fe-free nutrient solution to induce Fe starvation. Afterward, plants were cultivated for 6 days on two different calcareous soils. Total DNA was extracted from rhizosphere and bulk soil and 454 pyrosequencing technology was applied to V1-V3 16S rRNA gene region. Approximately 5000 sequences were obtained for each sample. The analysis of the bacterial population confirmed that the two bulk soils showed a different microbial community. The presence of the two plant species, as well as the nutritional status (Fe-deficiency and Fe-sufficiency), could promote a differentiation of the rhizosphere microbiome, as highlighted by non-metric multidimensional scaling (NMDS) analysis. Alphaproteobacteria, Actinobacteria, Chloracidobacteria, Thermoleophilia, Betaproteobacteria, Saprospirae, Gemmatimonadetes, Gammaproteobacteria, Acidobacteria were the most represented classes in all the samples analyzed even though their relative abundance changed as a function of the soil, plant species and nutritional status. To our knowledge, this research demonstrate for the first time that different plants species with a diverse nutritional status can promote the development of a peculiar rhizosphere microbiome, depending on the growth substrate.

The use of organic compost combined with inorganic fertilizer can enable balanced fertilization under intensive farming conditions, but little is known about how these fertilization practices affect the composition of microbial in arable soils. In this study, a field trial of a rice–wheat cropping system was established to examine the effects of 8 years of fertilization with inorganic fertilizers (IFs) and the organic manure–inorganic fertilizers (OMIFs) on composition of microbial communities. The fungal 18S and bacterial 16S rRNA gene fragments were amplified from each soil sample and sequenced. Significantly lower fungal richness and higher bacterial richness were observed for the OMIF treatment compared to the other treatments. No obvious changes in fungal diversity were observed among the treatments, with a decrease bacterial diversity detected in the IF treatment. Variations in relative abundance were observed in the fungal phyla Glomeromycota, Blastocladiomycota, and Schizoplasmodiida and in the bacterial phyla Acidobacteria, Gemmatimonadetes, and Cyanobacteria, most of which were significantly correlated with soil organic matter (OM) and/or nitrate N (NO3 −-N) contents. Additionally, the fungal abundance-based coverage estimator (ACE) showed a significant negative correlation with the soil NO3 −-N/OM content, while the correlation was positive for the bacterial ACE estimate. This study suggests that the fungal and bacterial communities respond differently to the long-term organic-inorganic fertilization, which may result from different effects of NO3 −-N/OM content of soil on the composition of fungal and bacterial communities.

Gemmatimonadetes represents a poorly understood bacterial phylum with only a handful of cultured species. Recently, one of its few representatives, Gemmatimonas phototrophica, was found to contain purple bacterial photosynthetic reaction centres. However, almost nothing is known about the environmental distribution of phototrophic Gemmatimonadetes bacteria. To fill this gap, we took advantage of fast-growing public metagenomic databases and performed an extensive survey of metagenomes deposited into the NCBI's WGS database, the JGI's IMG webserver and the MG-RAST webserver. By employing Mg protoporphyrin IX monomethyl ester oxidative cyclase (AcsF) as a marker gene, we identified 291 AcsF fragments (24-361 amino acids long) that are closely related to G. phototrophica from 161 metagenomes originating from various habitats, including air, river waters/sediment, estuarine waters, lake waters, biofilms, plant surfaces, intertidal sediment, soils, springs and wastewater treatment plants, but none from marine waters or sediment. Based on AcsF hit counts, phototrophic Gemmatimonadetes bacteria make up 0.4-11.9% of whole phototrophic microbial communities in these habitats. Unexpectedly, an almost complete 37.9 kb long photosynthesis gene cluster with identical gene composition and arrangement to those in G. phototrophica was reconstructed from the Odense wastewater metagenome, only differing in a 7.2 kb long non-photosynthesis-gene insert. These data suggest that phototrophic Gemmatimonadetes bacteria are much more widely distributed in the environment and exhibit a higher genetic diversity than previously thought.

Baikalian sponges are unique organisms with many species harboring symbiotic microbes that produce novel bioactive compounds. To investigate bacterial diversity of three species of Baikalian sponges, specimens of Lubomirskia baicalensis , Baikalospongia intermedia and Swartschewskia papyracea collected from Lake Baikal were processed by pyrosequencing. We found differences in the species composition and diversity in bacteria among these sponges. Cyanobacteria accounted for the highest proportion and the second group was Proteobacteria in three sponges. The bacterial communities in B. intermedia and L. baicalensis were highly similar but less similar to the bacterial community associated with S. papyracea. Diversity of the bacterial community in S. papyracea was higher than in L. baicalensis and B. intermedia . In particular, the relative abundance of Actinobacteria was higher in S. papyracea . Bacterial species in phyla Acidobacteria and Gemmatimonadetes were only found in S. papyracea .

Investigating the microbial community structure and composition of toxic industrial wastes contaminated with nitrocellulose and various by-products is crucial for understanding the fate of these pollutants in the environment and for the development and application of effective bioremediation processes. In this study, we investigated the chemical properties and toxic potential of wastewater generated during nitrocellulose production. The analyzed wastewater from settling pond contained nitrocellulose powder particles as well as increased ammonium (570–760 mg/L), sulfate (1625–2045 mg/L) and sulfite (864–1014 mg/L) concentrations. The toxicity test results demonstrated that the wastewater samples present acute toxicity for Paramecium caudatum and Daphnia magna. Furthermore, bacterial community structure in the samples was characterized by pyrosequencing of 16S rRNA genes. Phylogenetic analysis of bacterial sequences indicated that Proteobacteria, Bacteroidetes and Firmicutes were the main phyla in the sample near inlet, whereas various phylotypes of the phyla Proteobacteria, Chlorobi, Bacteroidetes and Gemmatimonadetes dominated in the sample near outlet. Some bacterial members observed in the current work can be considered as agents capable of performing biodegradation of various hazardous contaminants, indicating that the described bacterial communities have a high potential for the development of effective bioremediation strategies.

Soil microorganisms and their interactions with environmental factors govern critical ecosystem processes. However, the changes of soil microbial communities (e.g., relative abundance changes of different phylotypes) and the links between specific environmental factors and microbial communities are not well understood. We applied high-throughput sequencing of 16S rRNA gene amplicons to investigate the effects of mineral fertilizers P (superphosphate), N (urea), and NP and organic manure fertilizer (M) and its combined with mineral fertilizers (NM, PM, NPM) on bacterial and archaeal communities in rain-fed winter wheat soils in a 30-year experiment in the Loess Plateau of northwest China. Dramatic changes of soil respiration and the concentrations of total organic C, total N, and microbial biomass C and N were found in manure application soils (M, NM, PM, NPM) and some of them in NP soil. Soil microbial community structure shifted after fertilization, and a significant difference of prokaryotic community structure was found between mineral fertilizer soils (P, N, and NP) and manure application soils (M, NM, PM, NPM) except the soils between PM and P. The prokaryotic community structure in M soil was different from that in NM and NPM soils and differed between N and P and NP soils. Acidobacteria, Actinobacteria, and Proteobacteria were the predominant phyla (55.5–76.5 % of abundance) and, together with some other phyla, were changed by fertilization at the phylum or lower taxon ranks. No fertilizer soil had the highest relative abundances of phyla WS3 and Gemmatimonadetes. P soil changed the relative abundances of phyla Acidobacteria, Gemmatimonadetes, and Verrucomicrobia, but only enriched the bacteria at the family level (Micrococcaceae) when combined with N or M application (NP, PM, and NPM). Some copiotrophic bacteria showed different responses to nitrogen and manure applications, e.g., Actinobacteria increased in abundance in nitrogen application soils (N, NP, NM, and NPM), whereas Bacteroidetes and Gammaproteobacteria increased in abundance in manure application soils (M, NM, PM, and NPM). The above patterns of the relative abundance vs nitrogen or manure application were correlated to soil C and N contents or C/N ratio. These results supported the hypothesis that different bacterial taxa would be favorable in P, N, and manure application soils and suggested that the changes of bacteria taxa in fertilized soils appeared to be more driven by nitrogen and manure applications than P application.

Salinization is a matter of growing concern as it decreases plant productivity in degraded grassland soils; however, its effects on bacterial and fungal communities remain unknown. Therefore, we used the next-generation sequencing technology of soil bacterial 16S rRNA and fungal internal transcribed spacer (ITS) to investigate the diversities and structures of soil bacterial and fungal communities under four different salinity or electrical conductivity (EC) conditions. Our results showed that high salinity increased the relative abundance of Gemmatimonadetes and Bacteroidetes, but, decreased that of Proteobacteria and Firmicutes. In addition, high soil salinity increased the relative abundance of the fungal phylum Ascomycota. The soil pH value significantly increased as the soil salinity increased. Structural equation models (SEMs) showed that soil pH and EC had a total impact on the soil total microbial diversity and basic respiration. Increasing soil pH directly decreased the soil total Shannon diversity and basic respiration according to the SEMs. In contrast, increasing the soil EC directly increased soil total Shannon diversity and decreased soil basic respiration. Soil pH was negatively correlated with both bacterial and fungal diversity compared with soil EC in the SEMs. Our results indicate the opposite effects between soil bacterial and fungal diversity on soil microbial respiration in the highly saline grassland soils.

Alpine meadow degradation induced by human trampling decreases plant biomass and species diversity, potentially altering soil chemistry and microbial community composition. We studied soil carbon (C), nitrogen (N) and phosphorus (P) plus soil bacterial and fungal community structure in alpine meadows, along a degradation gradient induced by human trampling at Wugong Mountain, China. As degradation increased (from 0 to 100% bare ground), pathotroph (both animal and plant hosts) and symbiotroph (especially ectomycorrhizae) fungal diversity increased but overall microbial diversity did not vary. Degradation altered fungal taxonomic composition with higher Cryptomycota and Mucoromycota diversity in more degraded sites. Path analyses indicated that fungal composition changes with degradation were mainly related to changes in soil C and P while bacterial changes were mainly related to changes in soil N and pH. Degradation modified bacterial taxonomic composition with higher Gemmatimonadetes but lower Acidobacteria, Cyanobacteria, and Planctomycetes diversity associated with lower pH, higher TN, lower NH4+, and higher NO3− in more degraded areas. The results indicate that trampling impacts both soil fungal and bacterial communities but these microbial groups respond to different soil chemistry modifications. These results highlighting soil microbial community changes suggest their importance in the restoration of degraded alpine meadows with human trampling and hence the rapid recovery of their function.

The widely distributed seaweed Ulva fasciata has nutrient absorption abilities and can be used in the bioremediation of polluted maricultural environments. This study explored microbial community and antibiotic resistance gene (ARG) variation in mariculture sediments in response to different trace levels (10, 100, and 500 μg L−1) of oxytetracycline (OTC) and the presence of Ulva fasciata. The increase in OTC level promoted nutrient (NO3_-N and PO43--P) removal mainly due to Ulva fasciata adsorption. The abundances of the Euryarchaeota and Planctomycetes phyla in sediments were positively related to the increase in OTC stress, while a negative correlation occurred for the Proteobacteria phylum via metagenomic analysis. Compared with the control system, the increase rates of total ARGs were 3.90%, 7.36% and 13.42% at the OTC levels of 10, 100 and 500 μg L−1, respectively. OTC stress mainly favoured the collateral enrichment of non-corresponding polypeptide and MLS ARGs, mainly due to the enrichment of the phyla Planctomycetes and Euryarchaeota by the synergistic effect of OTC and nutrients. The results of quantitative PCR with tetracycline resistance genes (TRGs) (tetO, tetT, tetPB, tetW and otrA) and a horizontal transfer gene (intl1) demonstrated that all of genes had much higher gene numbers in sediments after 3 months of OTC stress than in those without OTC stress, which was strongly related to the variation in the phyla Bacteroidetes, Gemmatimonadetes and Acidobacteria. The significant correlation between intl1 and the target TRGs is indicative of the important role of the horizontal transfer of integron-resistant genes in the spread of TRGs.

We studied the influence of phosphorus (P) fertilizers on bacterial communities at different P fertilizer dosages (60 and 120 kg/ha) and delivery systems (row and broadcast application) in a wheat field in China. The bacterial community composition was identified using 16S rRNA high-throughput sequencing analysis. The input of phosphate fertilizer changed the diversity and distribution of the bacterial community in the soil layers. The influence on the 0–20 cm layer was greater than that on the 20–40 cm layer. The abundance of Bacteroidetes and Proteobacteria was enriched in TT60, and the predominant phyla were Proteobacteria (48.69 %), Acidobacteria (23.11 %), Bacteroidetes (20.67 %), Actinobacteria (19.21 %), Gemmatimonadetes (12.03 %) and Chloroflexi (8.05 %). P fertilization increased the abundance and activity of functional degrading bacteria. Oligotrophic bacteria tended to be replaced by copiotrophs under P fertilization treatment. A greater effect was observed in the 0–20 cm layer compared to the 20–40 cm soil layer and also for 60 kg/ha P applied by row application. Correlation redundancy analysis demonstrated pH, organic matter (OM) and available phosphorus (AP) were the dominant contributors to the shift of bacterial community along with phosphorus fertilization strategy. P is a major variable that regulates microbial distribution by stimulating carbon-phosphorus coupling and participating in nitrogen-phosphorus synergy action to relate bacterial, aiming to make bacteria interrelated, and further alter carbon-phosphorus-nitrogen metabolism. Our results will further improve our understanding of how fertilizer measures affect soil quality by changing soil microbial communities in semi-arid agricultural ecosystems.

Fertilization is one of the most common agricultural practices to achieve high yield. Although microbes play a critical role in nutrient cycling and organic matter decomposition, knowledge of the long-term responses of the soil bacterial community to organic and inorganic fertilizers is still limited. This study was conducted to evaluate the effects of century-long organic (manure), inorganic (NPK), and no fertilization (control) treatments on soil bacterial community structure under continuous winter wheat (Triticum aestivum L.) cultivation. Fertilization treatments altered the richness, diversity and composition of the soil bacterial community. Compared with the control, manure significantly increased the operational taxonomic units (OTUs), Chao 1 and Shannon indices, and taxonomic groups, while NPK significantly decreased these parameters. Fertilization treatments did not alter the types of dominant phyla but did significantly affect their relative abundances. Acidobacteria and Proteobacteria were the most dominant phyla in all treatments. Manure led to enrichment of most phyla, with a diazotrophic group, Cyanobacteria, being an exception, NPK reduced most phyla, but enriched Chloroflexi, control led to promotion of Cyanobacteria. Soil pH and NO3&minus, were two dominant parameters influencing the bacterial community structure. Soil pH positively correlated with the relative abundances of Proteobacteria and Gemmatimonadetes but negatively correlated with those of Acidobacteria and Chloroflexi, NO3&minus, negatively correlated with the relative abundance of Cyanobacteria, which was 14&ndash, 52 times higher in control than the fertilized soils. Cyanobacteria, especially M. paludosus and L. appalachiana, could be the key players in maintaining wheat productivity in the century-long unfertilized control.

Gut microbiota executes many beneficial functions. In this study, the relationship between gut microbiota and ovarian development in the swimming crab P. trituberculatus was explored for the first time. A total of 28 phyla and 422 genera were identified across all samples. However, 105 differential operational taxonomic units, and four differential phyla (Gemmatimonadetes, Actinobacteria, Firmicutes, Marinimicrobia_(SAR406_clade)) were identified. At the genus level, 42 differential genera were identified and 144 bacterial indicators were identified. A key finding was that the relative abundance of 139 indicator bacteria detected in the anisomycin-2 mg/kg group (AK group) was higher than that of blank group (BK group), control group (CK group), SP600125-15 mg/kg group (SK group). In addition, the relative abundance of three indicator bacteria (OTU_236, OTU_1395, OTU_552) detected in the SK group was higher than that of the BK, CK and AK groups. It was also found that the relative abundance of 20 differential genera (Methyloversatilis, Coprococcus_1, Erysipelotrichaceae_UCG_003, Rikenella, Corynebacterium, Ruminiclostridium, Fusicatenibacter, [Eubacterium]_ruminantium_group, Rikenellaceae_RC9_gut_group, Bifidobacterium, Lachnospiraceae_NK4A136_group, Ruminococcaceae_UCG_014, Christensenellaceae_R_7_group, uncultured_Bacteroidales_bacterium, Coprococcus_2, Desulfovibrio, Aggregatibacter, Ambiguous_taxa, Alloprevotella and Ruminococcaceae_NK4A214_group) in the SK, BK, CK, and AK group samples were increasing. These differential genera may reveal the relationship between gut microbial communities and ovarian development in P. trituberculatus after injection with the JNK pathway inhibitor SP600125 or the activator anisomycin. In summary, this study provides a new understanding into the relationship between gut microbiota and ovarian development in response to stimulation with inhibitor or activator.

Bacterial community structure was analysed from the coastal and offshore surface waters of the Bay of Bengal (BoB) using of Next Generation Sequencing (NGS) approach. Taxonomic richness was high in the offshore waters compared to the coastal waters. Analysis of sequence data revealed that both the offshore and coastal waters in our study were dominated by Proteobacteria (67.14% and 61.91%, respectively). The most dominant genera in the coastal waters were Synechococcus, Erythrobacter, Psychrobacter while Prochlorococcus, and Vibrio were dominant in the offshore waters. Interestingly, the distribution of minor phyla was distinctly different in coastal and offshore environments. Fusobacteria, Synergistetes, Fibrobacteres, Spirochaetes, Gemmatimonadetes, Chlorobi, Chlamydiae, and Armatimonadetes were the minor phyla (6.84%) present in offshore waters. The metabolic predictions of the bacterial communities revealed distinctly different activities in the coastal and offshore water samples, which could be attributed to the differences in the physico-chemical conditions and substrate availability. Major functions included sulfate reduction, oxalic acid degradation, dehalogenation, nitrite reduction, ammonia oxidation, nitrogen fixation, xylan degradation, and aromatic hydrocarbons degradation.

Perfluorinated compounds (PFCs) contamination of soil has attracted global attention in recent years but influences of PFCs on microorganisms in the soil environment have not been fully described. In this study, the effects of perfluorooctane sulphonate (PFOS) and perfluoroctanoic acid (PFOA) on bacterial communities were determined by Illumina Miseq sequencing and Illumina Hiseq Xten. The stimulation of PFCs pollutants on soil bacterial richness and community diversity were observed. Sequencing information indicated that Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Gemmatimonadetes were the dominant bacterial phyla. Two genera, Bacillus and Sphingomonas, exhibited adverse responses toward PFCs pollution. Carbohydrate-active enzymes (CAZy), Kyoto Encyclopedia of Genes and Genomes (KEGG) and NCBI databases were used to elucidate the proteins and function action of soil microbial to PFCs pollution. Pathways such as Carbohydrate metabolism, Global and overview maps and Membrane transport in the soil microbes were affected by PFCs stress. CAZy analysis revealed that glycosyl transferases (GTs) in PFCs-polluted soils showed more active, while glycoside hydrolases (GHs) were inhibited severely.

As an effective method to control soil erosion and increase vegetation coverage in the Loess Plateau of China, the conversion of cropland to plantations also influences soil respiration (Rs). A lot of research work has been performed on the response of Rs to land use change in this region. Nevertheless, the microbiological mechanism on the response of Rs to land use change has not been elucidated. In this study, Rs was measured during the conversion of cropland to plantations. Moreover, soil microbial community and metabolic function were analyzed by metagenomic sequencing. When the conversion of cropland to plantations was implemented, Rs significantly increased. Metagenomic analysis indicated that the conversion of cropland to plantations had a stronger impact on microbial abundance than microbial composition, which was reflected in the abundance of dominant phyla, such as Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Cyanobacteria, Gemmatimonadetes, Planctomycetes and Verrucomicrobia. Carbon metabolic pathways and genes also had a remarkable response to land use change. Although the abundance of some carbon metabolic genes decreased with the conversion of cropland to plantations, the abundance of CAZy (Carbohydrate-Active Enzymes) genes increased. Moreover, carbon metabolic genes with significant differences affiliated to above dominant phyla. All results indicated that the conversion of cropland to plantations changed microbial abundance, which in turn affected abundance of carbon metabolic and CAZy genes. The increase in the storage of organic matter caused by the above changes promoted microbial catabolism for producing a large amount of CO2 in plantations soil, which was reflected by high Rs. Our study provides insights into the microbiological mechanism on the response of Rs to land use change during the conversion of cropland to plantations in the Loess Plateau of China. Keywords: Soil respiration, Microbial function, Microbial community, Metagenomics, Land use change, Loess plateau