Phylum Acidobacteria Research Articles

How arsenic contamination influences downslope wetland plant and microbial community structure and function

Mine tailings are prevalent worldwide and can adversely impact adjacent ecosystems, including wetlands. This study investigated the impact of gold (Au) mine tailings contamination on peatland soil and pore water geochemistry, vegetation and microbial communities, and microbial carbon (C) cycling. Maximum arsenic (As) concentrations in peat and pore water reached 20,137 mg kg−1 and 16,730 μg L−1, respectively, but decreased by two orders of magnitude along a 128 m gradient extending from the tailings into the wetland. Carbon and other macronutrient (N, P, K) concentrations in peat and pore water significantly increased with distance from contamination. Relative percent cover and species richness of vascular and non-vascular plants significantly increased with distance into the wetland, with higher non-vascular richness being found at intermediate distances before transitioning to a vascular plant dominated community. Bacterial and archaeal community composition exhibited a decreased proportion of members of the phylum Acidobacteria (notably of the order Acidobacteriales) and increased diversity and richness of methanogens across a larger range of orders farther from the tailings source, an indication of microbial C-cycling potential. Consistent with changes in microbial communities, in vitro microbial CH4 production potential significantly increased with distance from the contaminant source. This study demonstrates both the profound negative impact that metalliferous tailings contamination can have on above and belowground communities in peatlands, and the value of wetland preservation and restoration.

Microbial communities of biochar amended forest soils in northwestern USA

Biochar is an environmental soil application tool used for climate change mitigation and carbon (C) sequestration that can be used in forest soils. Soil physical and chemical properties can be altered by biochar amendment, which can affect soil microbial communities. A limited number of forest soil studies have shown biochar can affect soil microbial communities, but few studies exist in temperate, northwestern USA forests. We investigated the effects of biochar amendment to soil in three western USA managed forest sites. Sites were amended with 0, 2.5, or 25 Mg ha−1 biochar, applied to the soil surface. DNA was extracted from soil samples collected from two depths, three to five years following amendment (dependent on site). Double-barcoded 16S rRNA (bacteria) and LSU rRNA (fungi) amplicons were sequenced on an Illumina MiSeq platform. Resulting sequencing data was analyzed for community richness, diversity, phyla relative abundance, and composition. For fungi, sequencing data represented six phyla. Biochar amendment did not affect fungal community measures, but site and sampling depth or their interaction did. Bacterial sequencing data represented 33 phyla. Biochar did not affect richness or diversity measures. However biochar did affect Bacteroidetes and Acidobacteria phyla relative abundance either alone, or when dependent on site or sampling depth. As with fungi, site and sampling depth or their interaction influenced richness, diversity, phyla relative abundance, and community composition. Results indicate that biochar amendment to northwestern USA forests is not detrimental to soil microbial community composition.

Effect of Dioscorea Opposite Waste Supplementation on Antioxidant Capacity, Immune Response and Rumen Microbiome in Weaned Lambs

Dioscorea opposite waste (DOW) has been shown to improve the gastrointestinal microbiome, antioxidation capacity, and immune activity, indicating it is a potential feed resource to improve the physiological health and rumen function of weaned lambs. In the present study, the responses of rumen microbiome to DOW supplementation in diet were profiled using metagenome sequencing. In addition, the potential of DOW to regulate plasma parameters in weaned lambs and its possible mechanisms were investigated. Sixty healthy male small tail Han lambs (22.68 ± 2.56 kg) were selected and equally assigned to four dietary treatments: (1) DOW-free diet (CON), (2) addition of 10% DOW diet (DOW1), (3) addition of 15% DOW diet (DOW2), and (4) addition of 20% DOW diet (DOW3). Experimental lambs were fed a corresponding diet for 62 days. Rumen microbiome and plasma parameters were determined at the end of the experiment. The results showed that dietary supplementation with DOW linearly increased the concentration of aspartate aminotransferase, alkaline phosphatase, Immunoglobulin A, Immunoglobulin M, Immunoglobulin G, Glutathione peroxidase, Superoxide dismutase, and total antioxidant capacity in the plasma of weaned lambs, but an opposite trend was observed in Interleukin-1β, Interleukin-6, tumor necrosis factor-α, and Malondialdehyde between the DOW-supplemented group and the CON group. Sequencing of rumen metagenome revealed that dietary supplementation with 20% DOW significantly affected the microbial composition and function and increased the richness and diversity of rumen microbiota and relative abundance of phylum Verrucomicrobia, Planctomycetes, Fibrobacteres, Chloroflexi, Actinobacteria, and Acidobacteria and species Ruminococcaceae_bacterium, Clostridiales_bacterium_NK3B98, Clostridiales_bacterium, and Clostridia_bacterium. It was concluded that supplementing the weaned lamb’s ration with DOW increased the immune response and antioxidant capacity in a dose-dependent manner. Meanwhile, dietary supplementation with 20% DOW modulated the composition of rumen microbiome function by increasing Ruminococcaceae_bacterium and Clostridiales_bacterium with improving the polysaccharide hydrolase activity in the rumen.

Nitrogen removal performance and bacterial community analysis of a multistage step-feeding tidal flow constructed wetland

A multistage mesocosm vertical flow constructed wetland system was designed to treat synthetic domestic wastewater with a high nitrogen (N) load. The study aim was to determine the impact of design and operational variables on N removal efficiency in such systems. A tidal flow operational strategy enhanced aeration and was coupled with a step-feeding approach to promote N removal. Over the 420-day running period N removal rates were between 70 and 77 gN/m3/d, for a step-feeding ratio range of 60:40 to 80:20. The system was able to remove 91–95% of chemical oxygen demand, 74–91% of ammonium and 66–81% of total-N. Tidal flow and step-feeding strategies significantly impacted nitrogen removal with the best performance at a step-feeding ratio of 80:20 providing a carbon to nitrogen (COD/N) ratio of 4–5. The bacterial diversity increased at each stage throughout the system with dominating phyla Proteobacteria, Firmicutes, Planctomycetes, Bacteroidetes, Chloroflexi, Verrucomicrobia and Acidobacteria. Dominant bacteria at the genus level were Thiothrix, Planctomyces, Azonexus, Pseudoxanthomonas, Hydrogenophaga, Gemmobacter and other genera suggesting that N removal was accomplished via diverse metabolic pathways, including autotrophic nitrification, heterotrophic denitrification, autotrophic denitrification, and possibly anammox. This study shows benefits of step-feeding strategies in tidal flow constructed wetlands as a cost-effective solution for minimizing external carbon input to achieve effective N removal.

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress.

Soil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear. This study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress. Compared to the control (treated with ddH2O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.

Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings.

Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.

The shift of soil microbial community induced by cropping sequence affect soil properties and crop yield.

Rational cropping maintains high soil fertility and a healthy ecosystem. Soil microorganism is the controller of soil fertility. Meanwhile, soil microbial communities also respond to different cropping patterns. The mechanisms by which biotic and abiotic factors were affected by different cropping sequences remain unclear in the major grain-producing regions of northeastern China. To evaluate the effects of different cropping sequences under conventional fertilization practices on soil properties, microbial communities, and crop yield, six types of plant cropping systems were performed, including soybean monoculture, wheat-soybean rotation, wheat-maize-soybean rotation, soybean-maize-maize rotation, maize-soybean-soybean rotation and maize monoculture. Our results showed that compared with the single cropping system, soybean and maize crop rotation in different combinations or sequences can increase soil total organic carbon and nutrients, and promote soybean and maize yield, especially using soybean-maize-maize and maize-soybean-soybean planting system. The 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing showed that different cropping systems had different effects on bacterial and fungal communities. The bacterial and fungal communities of soybean monoculture were less diverse when compared to the other crop rotation planting system. Among the different cropping sequences, the number of observed bacterial species was greater in soybean-maize-maize planting setup and fungal species in maize-soybean-soybean planting setup. Some dominant and functional bacterial and fungal taxa in the rotation soils were observed. Network-based analysis suggests that bacterial phyla Acidobacteria and Actinobacteria while fungal phylum Ascomycota showed a positive correlation with other microbial communities. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) result showed the presence of various metabolic pathways. Besides, the soybean-maize-maize significantly increased the proportion of some beneficial microorganisms in the soil and reduced the soil-borne animal and plant pathogens. These results warrant further investigation into the mechanisms driving responses of beneficial microbial communities and their capacity on improving soil fertility during legume cropping. The present study extends our understanding of how different crop rotations effect soil parameters, microbial diversity, and metabolic functions, and reveals the importance of crop rotation sequences. These findings could be used to guide decision-making from the microbial perspective for annual crop planting and soil management approaches.

Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data

BackgroundGut dysbacteriosis has been reported as one of the etiologies for irritable bowel syndrome (IBS). However, the association between gut microbiota and IBS is still inconclusive.MethodA paired-sample study was designed by retrieving original multicenter 16 s-rRNA data of IBS patients and healthy controls from the GMrepo database. The propensity score matching (PSM) algorithm was applied to reduce confounding bias. The differential analysis of microbiota composition was performed at different taxonomic levels. The co-occurrence network was established. Subgroup analysis was performed to identify specific microbial compositions in different IBS subtypes.ResultsA total of 1522 amplicon samples were initially enrolled. After PSM, 708 individuals (354 IBS and 354 healthy controls) were eligible for further analysis. A total of 1,160 genera were identified. We identified significantly changed taxa in IBS groups (IBS-enriched: the families Enterobacteriaceae, Moraxellaceae and Sphingobacteriaceae; the genera Streptococcus, Bacillus, Enterocloster, Sphingobacterium, Holdemania and Acinetobacter. IBS-depleted: the phyla Firmicutes, Euryarchaeota, Cyanobacteria, Acidobacteria and Lentisphaerae; the families Bifidobacteriaceae, Ruminococcaceae, Methanobacteriaceae and the other 25 families; the genera Faecalibacterium, Bifidobacterium and other 68 genera). The co-occurrence network identified three hub genera and six hub species (including Faecalibacterium prausnitzii) that may be involved in IBS pathophysiology. Strong positive interactions were identified among the Bifidobacterium longum, Bifidobacterium breve and Bifidobacterium adolescentis in the Bifidobacterium community.ConclusionThis study provides quantitative analysis and visualization of the interaction between the gut microbiota and IBS. The identification of key species should be further validated to evaluate their causal relationships with the pathogenesis of IBS.

Evaluation of bacterial diversity in a swine manure composting system contaminated with veterinary antibiotics (VAs).

Composting has become an alternative for the treatment of organic effluents, due to its low cost, easy handling, and a great capacity for treating swine manure. As it is a biological process, many microorganisms are involved during the composting process and act in the degradation of organic matter and nutrients and also have the ability to degrade contaminants and accelerate the transformations during composting. The objective of this work was to identify microorganisms present in the swine effluent composting system, under the contamination by most used veterinary drugs in Brazil. The composting took place for 150days, there was an addition of 200 L of manure (these 25 L initially contaminated with 17 antibiotics) in 25kg of eucalyptus wood shavings. The microorganisms were measured at times (0 until 150days) and were identified by the V3-V4 regions of the 16S rRNA for Bacteria, by means of next-generation sequencing (NSG). The results show seven different bacterial phyla (Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria, Actinobacteria, Spirochaetota and Tenericutes) and 70 bacterial genera (more than 1% significance), of which the most significant ones were Pseudomonas, Sphingobacterium, Devosia, Brucella, Flavisolibacter, Sphingomonas and Nitratireductor. The genus Brucella was found during mesophilic and thermophilic phases, and this genus has not yet been reported an in article involving composting process. With the results obtained, the potential for adaptation of the bacterial community was observed, being under the influence of antibiotics for veterinary use.

Structure and Functional Properties of Bacterial Communities in Surface Sediments of the Recently Declared Nutrient-Saturated Lake Villarrica in Southern Chile.

Lake Villarrica, one of Chile's main freshwater water bodies, was recently declared a nutrient-saturated lake due to increased phosphorus (P) and nitrogen (N) levels. Although a decontamination plan based on environmental parameters is being established, it does not consider microbial parameters. Here, we conducted high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR) analyses to reveal the structure and functional properties of bacterial communities in surface sediments collected from sites with contrasting anthropogenic pressures in Lake Villarrica. Alpha diversity revealed an elevated bacterial richness and diversity in the more anthropogenized sediments. The phylum Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria dominated the community. The principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed significant differences in bacterial communities of sampling sites. Predicted functional analysis showed that N cycling functions (e.g., nitrification and denitrification) were significant. The microbial co-occurrence networks analysis suggested Chitinophagaceae, Caldilineaceae, Planctomycetaceae, and Phycisphaerae families as keystone taxa. Bacterial functional genes related to P (phoC, phoD, and phoX) and N (nifH and nosZ) cycling were detected in all samples by qPCR. In addition, an RDA related to N and P cycling revealed that physicochemical properties and functional genes were positively correlated with several nitrite-oxidizing, ammonia-oxidizing, and N-fixing bacterial genera. Finally, denitrifying gene (nosZ) was the most significant factor influencing the topological characteristics of co-occurrence networks and bacterial interactions. Our results represent one of a few approaches to elucidate the structure and role of bacterial communities in Chilean lake sediments, which might be helpful in conservation and decontamination plans.

Understory ferns promote the restoration of soil microbial diversity and function in previously degraded lands

Microorganisms facilitate the recovery of previously degraded soils, such as degraded lands experiencing vegetation restoration and understory expansion, through vital soil functions like nutrient cycling and decomposing organic matter. Despite the role of microorganisms in recovery, little is known about the effects of the process on microbial diversity and function. Here, we performed an understory fern, Dicranopteris dichotoma (Thunb.) Berhn removal treatments nested within three Masson pine (Pinus massoniana L.) plantations with different restoration years in subtropical China. Three ferns treatments including no ferns cover, with ferns cover, and the ferns removal treatments were established to assess the impact of the ferns on soil microbial diversity and function during revegetation and drivers of observed changes. We combined high-throughput sequencing, network structure modeling, and function prediction of soil bacterial and fungal communities to determine microbial diversity and functions. Our results showed that soil bacterial and fungal diversity increased with restoration time. Understory ferns significantly increased soil microbial diversity in the un-restored land but the effect became smaller in two restored sites. Understory ferns significantly increased the relative abundance of bacterial phyla Proteobacteria and Acidobacteria, but decreased that of Chloroflexi and Firmicutes. Furthermore, the presence of ferns increased the abundance of Basidiomycota, but increased the abundance of Ascomycota. Co-occurrence network analysis revealed that the presence of ferns leads to more complex of bacterial networks with more connections, nodes, average degrees, betweenness, and degrees. The functional predictions indicate that aerobic chemoheterotrophy, chemoheterotrophy, and nitrogen fixation functional groups play key roles in the nutrient cycling of soils with ferns cover. The bacterial and fungal community compositions were strongly affected by revegetation and understory ferns as litter biomass and soil nitrogen were identified as the key environmental factors. Our study highlights the role of understory in facilitating microbial diversity and function recovery during degraded lands restoration.

Habitat type and host grazing regimen influence the soil microbial diversity and communities within potential biting midge larval habitats

BackgroundBiting midges (Culicoides spp.) are important vectors of diverse microbes such as viruses, protozoa, and nematodes that cause diseases in wild and domestic animals. However, little is known about the role of microbial communities in midge larval habitat utilization in the wild. In this study, we characterized microbial communities (bacterial, protistan, fungal and metazoan) in soils from disturbed (bison and cattle grazed) and undisturbed (non-grazed) pond and spring potential midge larval habitats. We evaluated the influence of habitat and grazing disturbance and their interaction on microbial communities, diversity, presence of midges, and soil properties.ResultsBacterial, protistan, fungal and metazoan community compositions were significantly influenced by habitat and grazing type. Irrespective of habitat and grazing type, soil communities were dominated by phyla Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria (Bacteria); Apicomplexa, Cercozoa, Ciliophora, Ochrophyta (Protists); Chytridiomycota, Cryptomycota (Fungi) and Nematoda, Arthropoda (Metazoa). The relative abundance of Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia (Bacteria); Apicomplexa, Lobosa (Protists); Ascomycota, Blastomycotina, Cryptomycota (Fungi); and Platyhelminthes (Metazoa) were significantly affected by grazing type. Of note, midge prevalence was higher in grazed sites (67–100%) than non-grazed (25%). Presence of midges in the soil was negatively correlated with bacterial, protistan, fungal and metazoan beta diversities and metazoan species richness but positively correlated with protistan and fungal species richness. Moreover, total carbon (TC), nitrogen (TN) and organic matter (OM) were negatively correlated with the presence of midges and relative abundances of unclassified Solirubrobacterales (Bacteria) and Chlamydomonadales (Protists) but positively with Proteobacteria and unclassified Burkholderiales (Bacteria).ConclusionsHabitat and grazing type shaped the soil bacterial, protistan, fungal and metazoan communities, their compositions and diversities, as well as presence of midges. Soil properties (TN, TC, OM) also influenced soil microbial communities, diversities and the presence of midges. Prevalence of midges mainly in grazed sites indicates that midges prefer to breed and shelter in a habitat with abundant hosts, probably due to greater accessibility of food (blood meals). These results provide a first glimpse into the microbial communities, soil properties and prevalence of midges in suspected midge larval habitats at a protected natural prairie site.

Continuous cropping of cut chrysanthemum reduces rhizospheric soil bacterial community diversity and co-occurrence network complexity

Long-term continuous cropping causes a significant decline in the quality of cut chrysanthemum (Chrysanthemum morifolium Ramat.), but the microbial mechanism behind it remains unclear. Here, we examined the impacts of different numbers of years of continuous cropping on the bacterial communities and enzymatic activities in the rhizospheric soil of cut chrysanthemum. Our results showed that continuous cut chrysanthemum cropping for 6 years (Y6) or 12 years (Y12) significantly decreased (P < 0.05) the soil respiration rate and enzymatic activities of alkaline phosphatase and β-glucosidase compared to cropping for only 1-year (Y1). 12 years of continuous cropping resulted in significant decreases in soil bacterial numbers and α-diversity (e.g., Shannon index). Continuous cropping treatments shifted the bacterial community composition, lowering the relative abundances of the phyla Proteobacteria and Acidobacteria and increasing the relative abundances of Actinobacteria and Chloroflexi. Moreover, continuous cropping reduced the bacterial network complexity relative to noncontinuous cropping. Structural equation modeling (SEM) showed that long-term continuous cropping significantly decreased the soil bacterial count and community diversity mainly because of the limitation of soil organic carbon and total nitrogen, which in turn led to a reduction in soil respiration. Overall, our results demonstrated that continuous cut chrysanthemum cropping for 12 years had negative impacts on soil bacterial diversity, community complexity and soil biological activity.

Comparison of Rhizospheric and Endophytic Bacterial Compositions between Netted and Oriental Melons.

To elucidate the biological mechanism of formation of the netted pattern in melons, the characteristics of the soil bacterial community structure in the rhizosphere and of the endophytic bacteria in the stems of netted melons were analyzed. High-throughput sequencing technology was used for the analysis of plant stem and soil samples collected from netted melons (NM) and oriental melons (OM). At the phylum level, Acidobacteria, Dependentiae, and Chloroflexi were the dominant endophytic bacteria in the stems of NM only. In addition, at the genus level, the soil bacteria enriched in the rhizospheres of NM and OM were different. Five unique dominant bacterial genera, including Gaiella, Actinoplanes, norank_f__Gemmatimonadaceae, Devosia, and Bradyrhizobium, were the dominant soil bacteria unique to the rhizosphere of NM. In contrast, Mycobacterium and unclassified_f__Acetobacteraceae were the dominant soil bacteria in the rhizosphere of OM. Moreover, Hyphomicrobium, Nocardioides, norank_f__norank_o__Gaiellales, Bryobacter, unclassified_f__Pseudonocardiaceae, Pseudolabrys, norank_f__Micropepsaceae, Ideonella, Mizugakiibacter, norank_f__Vermiphilaceae, unclassified_f__Xanthobacteraceae, Bacillus, and Pseudaminobacter were the dominant endophytic bacteria in the stems of NM. In contrast, Flavobacterium, Stenotrophomonas, unclassified_f__Burkholderiaceae, Paenibacillus, Bordetella, Hephaestia, and Ideonella were the dominant endophytic bacteria in the stems of OM. The specific substances (enzymes, proteins, endogenous hormones, etc.) secreted by unique rhizospheric and endophytic bacteria, such as Bacillus and Bradyrhizobium, may activate the promoters of genes. Therefore, the expression of genes can be regulated by unique rhizospheric and endophytic bacteria for formation or nonformation of netting in melons. IMPORTANCE The study of the differential structures and functions of rhizospheric and endophytic bacterial communities between netted melon and oriental melon treatments is investigated. Our findings make a significant contribution to the literature because they are the first step in coupling the study of rhizospheric and endophytic microbial community structure to reticulation formation in netted melon. Further, we believe that this research appears to be meaningful because it provides new insights into the mechanisms of reticulation formation in netted melon in modern agricultural production.

Latitude variations of soil bacterial community diversity and composition in three typical forests of temperate, northeastern of China

Soil bacteria are a crucial component of forest soil biodiversity and play important functions in numerous ecosystem processes. Hence, studying the variation of diversity and composition of soil bacteria between latitude gradients and the driving factors responsible for these differences is important for understanding the changes of soil bacteria. We used Illumina MiSeq sequencing of bacterial 16S rRNA to investigate the distribution pattern and driving factors of bacterial diversity and composition in temperate forest soils at three different latitudes in northeast China, with samples taken at low, middle and high latitude. Each sample area was located at a distance of 1,200 km. Our results indicate that the soil bacterial diversity decreased with increasing latitude. Members of the phyla Acidobacteria and Proteobacteria were the dominant in all investigated soils, the highest relative abundances of these phyla were: Acidobacteria and Proteobacteria in high-latitude forest, Rokubacteria and Actinobacteria in low-latitude forest. The dominant bacterial genera in the three different latitude forests were Candidatus_Solibacter, Bryobacter, Roseiarcus and Granulicella. Mean average temperature, soil pH and total nitrogen content were the key environmental factors shaping the soil bacterial diversity and composition in different latitudes of these temperate forests. The results of this study contribute to a deeper understanding and better predictions the latitudinal pattern of soil biodiversity.

Soil microbiota impact on Boletus edulis mycelium in chestnut orchards of different ages

Biotic factors (host plant age and soil microbiota) influencing Boletus edulis mycelium frequency and concentration have been investigated. The study was carried out in September, October and November 2018 and 2020, using six orchards of chestnut hybrid Castanea × coudercii of 40-, 10- and 3-years-old. Taxonomical identity of bacterial and fungal species was ascertained by DNA metabarcoding. Mycelium frequency and concentration of B. edulis were studied through quantitative PCR (qPCR) of soil samples. It was hypothesized that mature plants (40-years-old) have a greater soil microbiota associated at the rhizosphere, in comparison with young plants (10- and 3-years-old). This situation may reverberate on B. edulis mycelium that should be more abundant in 40-years-old orchards, also thanks to the higher number of beneficial interactions whit soil microbiota. It was found that host plant age significantly altered bacterial and fungal assemblages in both years. Bacterial fraction was dominated by the phylum Proteobacteria, Acidobacteria and Actinobacteria and showed a higher species richness and diversity in orchards of 10- and 3-years-old. Fungal phylum such as Basidiomycota was more abundant in 40- and 10-years-old orchards, whereas Ascomycota and Mortierellomycota were more abundant in the 10- and 3-years-old orchards. Mycelium frequency of B. edulis in soil samples was higher in 2020 (97 %) than in 2018 (19 %), although without differences between plant age and sampling month in each year. Boletus edulis mycelium concentration was higher in 2020 than in 2018, and in September 2020, whereas plant age did not have any effect. Of 173 bacterial taxa considered, the 12 %, 54 % and 82 % of the significant correlations with B. edulis mycelium concentration were found in 40-, 10- and 3-years-old orchards, respectively. On the other hand, of 180 fungal taxa, the 12 %, 24 % and 42 % of the significant correlations occurred in 40-, 10- and 3-years-old orchards, respectively. This investigation represents the first report about the role of soil microbiota on the ecology of B. edulis in Castanea agro-ecosystem.

Effects of biochar and vermicompost on microorganisms and enzymatic activities in greenhouse soil

The effects of different contents of biochar and vermicompost on the microbial and enzymatic activities of greenhouse soil were determined to provide a theoretical basis for improving the quality of greenhouse soil. The experiment was conducted in a greenhouse using potted tomatoes. Five treatments consisted of different amount ratios of organic amendments: 1% biochar (BC1), 3% biochar (BC3), 5% biochar (BC5), 3% vermicompost (VC3), and 5% vermicompost (VC5), with no addition of organic amendments as the control (CK). Compared with CK, the pH, organic matter content, and DOC concentration increased in treatment groups. The organic matter content of BC3 and BC5 significantly increased by 54.6% and 72.8%, respectively, and DOC concentration of BC3 significantly increased by 43.9%. Biochar and vermicompost significantly increased the diversity of bacterial and fungal communities in soil, as well as the abundance of Actinomycetes, Acidobacteria, Ascomycetes, and Aspergillus, and reduced the abundance of Aspergillus. The activities of urease and alkaline phosphatase were significantly increased, and the activity of nitrate reductase was inhibited in all treatment groups compared with CK. In addition, a highly significant positive correlation was observed among pH, Acidobacteria phylum abundance, and alkaline phosphatase activity in all treatments. DOC concentration was positively correlated with pH, organic matter content, Acidobacteria phylum abundance and alkaline phosphatase activity. Biochar and vermicompost were effective in improving the physicochemical properties of greenhouse soil, enhancing microbial diversity, and affecting enzymatic activities. Therefore, BC3 (3% biochar) had the most significant effect on community diversity and alkaline phosphatase and nitrate reductase activities. VC5 (5% vermicompost) had the best promotion effect on urease activity. This study highlights that biochar and vermicompost as organic amendments are recommended to improve the quality of greenhouse soils.

Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing.

Metagenomics studies have revealed tremendous viral diversity in aquatic environments. Yet, while the genomic data they have provided is extensive, it is unannotated. For example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage-host interactions. This study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. To this end, we used water and sediment samples collected from seven sites with varying contamination levels in the Ebrié Lagoon in Abidjan, Ivory Coast. The bacterial communities were characterized using the 16S rRNA metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with VirSorter and VIBRANT; (2) classified these contigs with MetaPhinder using the phage database (taxonomic annotation); and (3) predicted the phages' bacterial hosts with a machine learning-based tool: the Prokaryotic Virus-Host Predictor. The findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. Phage sequences assigned to the Microviridae family were widespread in sediment samples, whereas phage sequences assigned to the Siphoviridae, Myoviridae and Podoviridae families were predominant in water samples. In terms of bacterial communities, the phyla Latescibacteria, Zixibacteria, Bacteroidetes, Acidobacteria, Calditrichaeota, Gemmatimonadetes, Cyanobacteria and Patescibacteria were most widespread in sediment samples, while the phyla Epsilonbacteraeota, Tenericutes, Margulisbacteria, Proteobacteria, Actinobacteria, Planctomycetes and Marinimicrobia were most prevalent in water samples. Significantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16S rRNA metabarcoding and phage-host prediction were significantly similar. These results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data.

Metagenomic insights into the characteristics of soil microbial communities in the decomposing biomass of Moso bamboo forests under different management practices.

Considering the rapid growth and high biomass productivity, Moso bamboo (Phyllostachys edulis) has high carbon (C) sequestration potential, and different management practices can strongly modify its C pools. Soil microorganisms play an important role in C turnover through dead plant and microbial biomass degradation. To date, little is known about how different management practices affect microbial carbohydrate-active enzymes (CAZymes) and their responses to dead biomass degradation. Based on metagenomics analysis, this study analyzed CAZymes in three comparable stands from each Moso bamboo plantation: undisturbed (M0), extensively managed (M1), and intensively managed (M2). The results showed that the number of CAZymes encoding plant-derived component degradation was higher than that encoding microbe-derived component degradation. Compared with the M0, the CAZyme families encoding plant-derived cellulose were significantly (p < 0.05) high in M2 and significantly (p < 0.05) low in M1. For microbe-derived components, the abundance of CAZymes involved in the bacterial-derived peptidoglycan was higher than that in fungal-derived components (chitin and glucans). Furthermore, M2 significantly increased the fungal-derived chitin and bacterial-derived peptidoglycan compared to M0, whereas M1 significantly decreased the fungal-derived glucans and significantly increased the bacterial-derived peptidoglycan. Four bacterial phyla (Acidobacteria, Actinobacteria, Proteobacteria, and Chloroflexi) mainly contributed to the degradation of C sources from the plant and microbial biomass. Redundancy analysis (RDA) and mantel test suggested the abundance of CAZyme encoding genes for plant and microbial biomass degradation are significantly correlated with soil pH, total P, and available K. Least Squares Path Modeling (PLS-PM) showed that management practices indirectly affect the CAZyme encoding genes associated with plant and microbial biomass degradation by regulating the soil pH and nutrients (total N and P), respectively. Our study established that M2 and M1 impact dead biomass decomposition and C turnover, contributing to decreased C accumulation and establishing that the bacterial community plays the main role in C turnover in bamboo plantations.

Rhizosphere bacteria regulated arsenic bioavailability and accumulation in the soil–Chinese cabbage system

The accumulation of arsenic (As) in Chinese cabbage (Brassica rapa ssp. pekinensis) has recently been a source of concern for a potential risk to human health. It is unknown whether natural variations of As accumulation in different genotypes of Chinese cabbage are related to rhizobacterial characteristics. Experiments were conducted to investigate the mechanisms of rhizobacteria involving in As fates in a soil–Chinese cabbage system using various genotypes using high-throughput sequencing and quantitative PCR. There were significant differences in As accumulation in cabbage leaves between 32 genotypes, and genotypes of low-As-accumulation (LSA) and high-As-accumulation (HSA) were identified. The As concentrations in the shoots of LSA were 23.25 %, 24.19 %, 15.05 %, and 70.69 % lower than those of HSA in seedling stage (SS), rosette stage (RS), heading stage (HS), and mature stage (MS), respectively. Meanwhile, the relative abundances of phyla Patescibacteria (in RS), Acidobacteria and Rokubacteria (in HS) in the rhizosphere of LSA were 60.18 %, 28.19 %, and 45.38 % less than those of HSA, respectively. Additionally, both shoot-As and As translocation factor had significantly positive or negative correlations with the relative abundances of Rokubacteria or Actinobacteria. In LSA rhizosphere, the relative abundances of genera Flavobacterium (in SS), Ellin6055 and Sphingomonas (in HS) were 128.12 %, 83.69 % and 79.50 % higher than those of HSA, respectively. This demonstrated that rhizobacteria contribute to the accumulation and translocation of As in HSA and LSA. Furthermore, the gene copies of aioA and arsM in LSA rhizosphere were 25.54 % and 16.13 % higher than those of HSA, respectively, whereas the gene copies of arsC in LSA rhizosphere were 26.36 % less than those of HSA in MS, indicating that rhizobacteria are involved in As biotransformation in the soil. These results provide a comprehensive understanding of the relationship between characteristics of rhizobacterial communities and As variations in Chinese cabbage genotypes.