Phylum Chloroflexi Research Articles

Waterborne Cr3+ and Cr 6+ exposure disturbed the intestinal microbiota homeostasis in juvenile leopard coral grouper Plectropomus leopardus

BackgroundChromium (Cr) mainly has two stable forms: Cr3+ and Cr6+. Cr and its compound are widely used in the printing, dyeing, leather making, and metallurgy industry. They are evitably released into the environment and pose a significant threat to creatures, for instance, the excessive chromium (Cr) burden in the marine ecosystem is often harmful to fish. Intestinal microbiota greatly affects fish performance, but how waterborne Cr affects fish intestinal microbiota is unclear. To test the hypothesis that the waterborne Cr exposure could significantly affect fish’ intestinal microbiota homeostasis, and the effect was highly dependent on Cr concentration and speciation, the juvenile leopard coral grouper Plectropomus leopardus were exposed to waterborne Cr3+ and Cr6+ (0.1, 0.5 ppm) for 7 days, and the intestinal microbiota was determined by Amplicon sequencing of the 16S rRNA. ResultsIn all Cr treatment groups, the alpha diversity of intestinal microbiota communities of P. leopardus was decreased. The phyla Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi and Bacteroidetes were the dominant intestinal microbiota. The Chao index diversity significantly declined in Cr treatment group, indicating the intestinal microbiota community structure was changed. Among the dominant intestinal microbiota, Proteobacteria was most sensitive to Cr exposure, and it increased after xposure. The PICRUSt predicted that 0.5 ppm Cr3+ expousure caused metabolism disordered in the intestinal of P. leopardus. ConclusionsWaterborne Cr3+ and Cr6+ significantly disturbed intestinal microbiota homeostasis in P. leopardus, including their diversity, composition, and community structure. The metabolism level of intestinal microbiota in P. leopardus was decreased by Cr3+ exposure. High concentrations of Cr3+ may pose potential risks to the intestinal homeostasis of P. leopardus.

Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater.

Global water supplies are threatened by climate changes and the expansion of urban areas, which have led to an increasing interest in nature-based solutions for water reuse and reclamation. Reclaimed water is a possible resource for recharging aquifers, and the addition of an organic reactive barrier has been proposed to improve the removal of pollutants. There has been a large focus on organic pollutants, but less is known about multifunctional barriers, that is, how barriers also remove nutrients that threaten groundwater ecosystems. Herein, we investigated how compost- and woodchip-based barriers affect nitrogen (N) removal in a pilot soil aquifer treatment facility designed for removing nutrients and recalcitrant compounds by investigating the composition of microbial communities and their capacity for N transformations. Secondary-treated, ammonium-rich wastewater was infiltrated through the barriers, and the changes in the concentration of ammonium, nitrate, and dissolved organic carbon (DOC) were measured after passage through the barrier during 1 year of operation. The development and composition of the microbial community in the barriers were examined, and potential N-transforming processes in the barriers were quantified by determining the abundance of key functional genes using quantitative PCR. Only one barrier, based on compost, significantly decreased the ammonium concentration in the infiltrated water. However, the reduction of reactive N in the barriers was moderate (between 21 and 37%), and there were no differences between the barrier types. All the barriers were after 1 year dominated by members of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, although the community composition differed between the barriers. Bacterial classes belonging to the phylum Chloroflexi showed an increased relative abundance in the compost-based barriers. In contrast to the increased genetic potential for nitrification in the compost-based barriers, the woodchip-based barrier demonstrated higher genetic potentials for denitrification, nitrous oxide reduction, and dissimilatory reduction of nitrate to ammonium. The barriers have previously been shown to display a high capacity to degrade recalcitrant pollutants, but in this study, we show that most barriers performed poorly in terms of N removal and those based on compost also leaked DOC, highlighting the difficulties in designing barriers that satisfactorily meet several purposes.

Community structure and function of microbiomes in polluted stretches of river Yamuna in New Delhi, India, using shotgun metagenomics.

The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization have profoundly affected river microflora and their function thus its health. In this study, potential of whole-genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing) and Syntrophobacter fumaroxidans (sulphate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages was also noticed along the downstream river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e. Nakaseomyces, Aspergillus, Schizosaccharomyces and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase-peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most enriched pollution degrading enzymes in the polluted study sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.

Cultured and uncultured microbial community associated with biogas production in anaerobic digestion processes.

The search for sustainable development has increased interest in the improvement of technologies that use renewable energy sources. One of the alternatives in the production of renewable energy comes from the use of waste including urban solids, animal excrement from livestock, and biomass residues from agro-industrial plants. These materials may be used in the production of biogas, making its production highly sustainable and environmentally friendly. The present study aimed to evaluate the cultivated and uncultivated microbial community from a substrate (starter) used as an adapter for biogas production in anaerobic digestion processes. 16S rDNA metabarcoding revealed the domain of bacteria belonging to the phyla Firmicutes, Bacteroidota, Chloroflexi and Synergistota. The methanogenic group was represented by the phyla Halobacterota and Euryarchaeota. Through 16S rRNA sequencing of isolates recovered from the starter culture, the genera Rhodococcus (Actinobacteria phylum), Vagococcus, Lysinibacillus, Niallia, Priestia, Robertmurraya, Proteiniclasticum (Firmicutes phylum), and Luteimonas (Proteobacteria phylum) were identified, genera that were not observed in the metabarcoding data. The volatile solids, volatile organic acids, and total inorganic carbon reached 659.10gkg-1, 717.70gkg-1, 70,005.0gkg-1, respectively. The cultured groups are involved in the metabolism of sugars and other compounds derived from lignocellulosic material, as well as in anaerobic methane production processes. The results demonstrate that culture-dependent approaches, such as isolation and sequencing, and culture-independent studies, such as the Metabarcoding approach, are complementary methodologies that, when integrated provide robust and comprehensive information about the microbial communities involved in processes of the production of biogas in anaerobic digestion processes.

Harnessing of phytomicrobiome for developing potential biostimulant consortium for enhancing the productivity of chickpea and soil health under sustainable agriculture

The main aim of the present work was to explore culturable bacteria and to develop potential microbial consortium as bio-inoculants for enhancing plant productivity, nutritional content, and soil health. For this study, we selected two bacterial strains e.g., Enterobacter hormaechei (BHUJPCS-15) and Brevundimonas naejangsanensis (BHUJPVCRS-1) based on plant growth-promoting activities We developed a consortium of both strains and estimated plant growth promotion (PGP) activity which recorded significant better production of Indole-3-acetic acid (IAA) (61.53 μg/ml), siderophore (12.66%), ammonia (98.66 μg/ml), phosphate solubilisation (942.64 μg/ml), potassium solubilisation, and antagonistic activity against Fusarium sp. than individual bacterial strains. Bacterial consortium (E. hormaechei + B. naejangsanensis) treatment significantly enhanced plant growth attributes, grain yields, nutritional content in plant and seed, followed by E. hormaechei as compared to control. Seed treated with consortium recorded a significant increase in available N P K, enzymes and microbial communities in soils. Microbiome analysis revealed that the dominance of bacterial group and its functional properties is directly correlated with plant growth attributes, nutrient content, soil N P K, and enzyme activity. The relative abundance of bacterial phyla Proteobacteria (98%) was dominantly recorded in all treatments. The microbiome of seed and soil, treated with consortium (E. hormaechei + B. naejangsanensis) showed high amount of diversity of bacterial phyla Verrucomicrobia, Firmicutes, Bacteroidetes, Acidobacteria, Chloroflexi, and Proteobacteria than E. hormaechei (Firmicutes, Bacteroidetes, Chloroflexi and Proteobacteria) and control (Firmicutes, Bacteroidetes and Proteobacteria). In soil, root and shoot, E. hormaechei treatment enriched ligninolytic, nitrogen fixation, cellulolytic, nitrate ammonification among other pathways. The main finding is that the consortium treated seed of chickpea recorded significant enhancement of plant growth attributes, productivity, nutritional content, and soil health as well as microbial colonization in soil and seed part.

Biogas Production and Microbial Communities of Mesophilic and Thermophilic Anaerobic Co-Digestion of Animal Manures and Food Wastes in Costa Rica

Biomass generated from agricultural operations in Costa Rica represents an untapped renewable resource for bioenergy generation. This study investigated the effects of two temperatures and three mixture ratios of manures and food wastes on biogas production and microbial community structure. Increasing the amount of fruit and restaurant wastes in the feed mixture significantly enhanced the productivity of the systems (16% increase in the mesophilic systems and 41% in the thermophilic). The methane content of biogas was also favored at higher temperatures. Beta diversity analysis, based on high-throughput sequencing of 16S rRNA gene, showed that microbial communities of the thermophilic digestions were more similar to each other than the mesophilic digestions. Species richness of the thermophilic digestions was significantly greater than the corresponding mesophilic digestions (F = 40.08, p = 0.003). The mesophilic digesters were dominated by Firmicutes and Bacteroidetes while in thermophilic digesters, the phyla Firmicutes and Chloroflexi accounted for up to 90% of all sequences. Methanosarcina represented the key methanogen and was more abundant in thermophilic digestions. These results demonstrate that increasing digestion temperature and adding food wastes can alleviate the negative impact of low C:N ratios on anaerobic digestion.

Effect of remediation reagents on bacterial composition and ecological function in black-odorous water sediments

Black-odorous urban water bodies and sediments pose a serious environmental problem. In this study, we conducted microcosm batch experiments to investigate the effect of remediation reagents (magnesium hydroxide and calcium nitrate) on native bacterial communities and their ecological functions in the black-odorous sediment of urban water. The dominant phyla (Proteobacteria, Actinobacteria, Chloroflexi, and Planctomycetes) and classes (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, Actinobacteria, Anaerolineae, and Planctomycetia) were determined under calcium nitrate and magnesium hydroxide treatments. Functional groups related to aerobic metabolism, including aerobic chemoheterotrophy, dark sulfide oxidation, and correlated dominant genera (Thiobacillus, Lysobacter, Gp16, and Gaiella) became more abundant under calcium nitrate treatment, whereas functional genes potentially involved in dissimilatory sulfate reduction became less abundant. The relative abundance of chloroplasts, fermentation, and correlated genera (Desulfomonile and unclassified Cyanobacteria) decreased under magnesium hydroxide treatment. Overall, these results indicated that calcium nitrate addition improved hypoxia-related reducing conditions in the sediment and promoted aerobic chemoheterotrophy.

Chinese Torreya agroforestry alters the rhizosphere soil bacterial communities and potential functions

The agroforestry practice has been regarded as a practical land-use selection to improve the Torreya grandis cv. Merrillii plantation management benefits. However, the relative report about the variation of rhizosphere soil bacterial communities and the potential functions under T. grandis-based agroforestry systems is currently limited. In the present study, we investigated the variation of soil bacterial communities and potential functions under the T. grandis-based agroforestry systems (T. grandis intercropping with Polygonatum sibiricum, PT; T. grandis silvopasture with goose, GT), using the Illumina MiSeq platform conjoined with Functional Annotation of Prokaryotic Taxa (FAPROTAX) annotation. The findings indicated that both silvopasture and intercropping significantly increased soil pH, total nitrogen (TN), available nitrogen (NH4+-N and NO3−-N), and total potassium (K) in comparison to the monoculture. According to the relative abundances of bacterial communities in T. grandis rhizosphere, Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the dominant phyla. The intercropping and silvopasture showed a significant increase in phyla Chloroflexi and Verrucomicrobia and a decrease in phyla Proteobacteria and Rokubacteria. Besides, the intercropping significantly increased Actinobacteria compared to the monoculture. The result indicated that the different agroforestry systems formed distinct bacterial community structures. The bacterial functional structures shifted from nitrogen-utilizing bacteria to carbon-utilizing bacteria under silvopasture and intercropping. The soil available N (NH4+-N and NO3−-N), pH, and TN were the most critical variables that impact the bacterial community and functional structures. These findings demonstrate that the bacterial community and potential function structures shift significantly under the agroforestry systems, reflecting the shift in the soil ecosystems caused by the plant-soil-microorganism interaction. Our findings provide valuable information for understanding the response of bacteria to land-use changes and emphasize the influence of T. grandis-based agroforestry systems on soil bacteria.

Inoculation of Prickly Pear Litter with Microbial Agents Promotes the Efficiency in Aerobic Composting

Prickly pear (Rosa roxburghii Tratt), a shrub mainly distributed in South China, is an economically essential plant for helping the local people out of poverty. To efficiently provide sufficient nutrients to the plant in the soil for the ecological cultivation of prickly pear, we studied the aerobic composting of a prickly pear litter with three agents, including AC (Bacillus natto, Bacillus sp., Actinomycetes sp., Saccharomyces sp., Trichoderma sp., Azotobacter sp., and Lactobacillus sp.), BC (Bacillus subtilis, Lactobacillaceae sp., Bacillus licheniformis, Saccharomyces sp., and Enterococcus faecalis), and CC (Bacillus sp., Actinomycetes sp., Lactobacillaceae sp., Saccharomyces sp., and Trichoderma sp.) and a control without microbial agents. The results show that the physicochemical and microbial traits of three resultant prickly pear composts were different after the inoculation with AC, BC, or CC. The pH values of three composts ranged from 8.0 to 8.5, and their conductivity values were between 1.6 and 1.9 mS/cm. The seed germination index of all three composts exceeded 70%. The contents of volatile solids and organic matter of the three composts both decreased significantly. The BC maximally increased the total N (18%) of the compost, whereas the CC maximally increased the total P (48%) and total K (38%) contents. Contents of available P and available K of the three composts increased significantly, and the available N content in compost after BC inoculation increased by 16%. The physicochemical features showed that three composts were non-hazardous to plants, and the microbial agents improved nutrient availability. The richness, Chao1, and Shannon index in the bacterial communities of three composts increased significantly. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes bacterium became dominant in the three composts, whereas at the family level, Microscillaceae and A4b (phylum Chloroflexi) became the dominant groups. Abundant cellulose-degrading bacteria existed at the dominant phylum level, which promoted fiber degradation in composts. Organic matter and the available N content regulated the composting bacterium. The inoculants enhanced the efficiency of composting: agents B and C were more suitable exogenous inoculants for the composting of a prickly pear litter.

A novel and affordable bioaugmentation strategy with microbial extracts to accelerate the biodegradation of emerging contaminants in different media

This study describes a new bioaugmentation alternative based on the application of aqueous aerated extracts from a biomixture acclimated with ibuprofen, diclofenac and triclosan. This bioaugmentation strategy was assayed in biopurification systems (BPS) and in contaminated aqueous solutions to accelerate the removal of these emerging contaminants. Sterilized extracts or extracts from the initial uncontaminated biomixture were used as controls. In BPS, the dissipation of 90% of diclofenac and triclosan required, respectively, 60 and 108 days less than in the controls. The metabolite methyl-triclosan was determined at levels 12 times lower than in controls. In the bioaugmented solutions, ibuprofen was almost completely eliminated (99%) in 21 days and its hydroxylated metabolites were also determined to be at lower levels than in the controls. The plasmidome of acclimated biomixtures and its extract appeared to maintain certain types of plasmids but degradation related genes became less evident. Several dominant OTUs found in the extract identified as Flavobacterium and Fluviicola of the phylum Bacteroidetes, Thermomicrobia (phylum Chloroflexi) and Nonomuraea (phylum Actinobacteria), may be responsible for the enhanced dissipation of these contaminants. This bioaugmentation strategy represents an advantageous tool to facilitate in situ bioaugmentation.

Anoxic/oxic treatment without biomass recycle

The Anoxic/Oxic (A/O) process involves recirculating mixed liquor between its A and O tanks so that nitrate produced in the O tank can be used to for denitrification with influent COD in the A tank. Because biomass is recirculated along with nitrate, A/O operation leads to similar microbial communities in the A and O tanks, which may decrease the rates of denitrification and nitrification in each tank. Here, bench-scale experiments simulated this aspect of the A/O process by exchanging biomass between an anoxic flask and an oxic cylinder at exchange ratios of 0%, 20%, 30%, and 50%. Nitrification and denitrification rates were only 40% and 19% for 50% biomass exchange of that for no biomass exchange. Phylogenetic analysis documented that the microbial communities became much more similar with biomass exchange, and the finding was consistent with community composition in a full-scale A/O process in a municipal wastewater treatment plant. A two-stage vertical baffled bioreactor (VBBR) realized efficient total‑nitrogen removal in recirculation without biomass exchange. Average removals of COD and TN were respectively 6% and 22% higher for the two-stage VBBR than the conventional A/O process, but its hydraulic retention time (HRT) was 55% to 70% of the volume of a conventional A/O process treating the same influent wastewater. The VBBR was more efficient because its anoxic biofilm was enriched in denitrifying bacteria, while its oxic biofilm was enriched in nitrifying bacteria. For example, the phylum Chloroflexi was greater in the An-VBBR, while the phylum Proteobacteria was greater in the Ox-VBBR.

Successional Changes of Microbial Communities and Host-Microbiota Interactions Contribute to Dietary Adaptation in Allodiploid Hybrid Fish.

Host-microbiota interactions play critical roles in host development, immunity, metabolism, and behavior. However, information regarding host-microbiota interactions is limited in fishes due to their complex living environment. In the present study, an allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) was used to investigate the successional changes of the microbial communities and host-microbiota interactions during herbivorous and carnivorous dietary adaptations. The growth level was not significantly different in any developmental stage between the two diet groups of fish. The diversity and composition of the dominant microbial communities showed similar successional patterns in the early developmental stages, but significantly changed during the two dietary adaptations. A large number of bacterial communities coexisted in all developmental stages, whereas the abundance of some genera associated with metabolism, including Acinetobacter, Gemmobacter, Microbacterium, Vibrio, and Aeromonas, was higher in either diet groups of fish. Moreover, the abundance of phylum Firmicutes, Actinobacteria, and Chloroflexi was positively correlated with the host growth level. In addition, Spearman's correlation analysis revealed that the differentially expressed homologous genes in the intestine associated with cell growth, immunity, and metabolism were related to the dominant gut microbiota. Our results present evidence that host genetics-gut microbiota interactions contribute to dietary adaptation in hybrid fish, which also provides basic data for understanding the diversity of dietary adaptations and evolution in fish.

Analysis of microbial communities in Binh Chau hot spring through metagenomic DNA sequencing

Binh Chau hot spring locates in Bung Rieng commune, Xuyen Moc district, Ba Ria - Vung Tau province, and is the second hottest hot spring in Vietnam. Up to date, the microbial diversity of this hot spring has been mainly evaluated using the culture-dependent methods, thus, it could not be able to assess all of microorganisms there. In this report, the microbial community of Binh Chau hot spring was investigated by meta-analysis using Hiseq Illumina for sequencing. The results revealed that only 106,903 genes were annotated and 49,190 genes were unknown among 156,093 potential ORFs. The annotated genes consisted of 29,069 bacterial genes, 1,416 archaeal genes, 4 eukaryotic genes, 3 viral genes, and 76,411 unclassified genes. Among the annotated and classified genes, the microbial community of Binh Chau hot spring was characterized by the predominance of bacteria over archaea. At the phylum level, the most abundant phyla in Binh Chau hot spring were followed as Proteobacteria > Firmicutes > Cyanobacteria > Bacteroidetes > Planctomycetes > Thaumarchaeota > Actinobacteria > Euryarchaeota. These belonged mainly to the thermophilic group. A number of the phyla are reported to grow at high temperature, alkaline pH, and high salt concentrations. In addition to the culturable species, the metagenomic data is also indicated the presence of unculturable groups, for example phylum Acidobacteria and Chloroflexi of bacteria. The order Thermoplasmata, which is classified to class Thermoplasmatales of the phylum Euryarchaeota, as well as ultra-small cell and symbiotic archaea including phyla Parvarchaeota, Nanohaloarchaeota, and Nanoarchaeota were detected. The results in this study indicated an important insight into the microbial communities of Binh Chau hot spring, which revealed a promising thermophilic gene sources for their exploitation and conservation in Vietnam.

Biological phosphorus removal and its microbial community in a modified full-scale activated sludge system under dry and wet weather dynamics

Enhanced biological phosphorus removal (EBPR) performance and microbial community dynamics during dry and wet-weather conditions of a full-scale treatment plant was evaluated by converting a section of activated sludge basins using low-cost operational modifications into an anoxic/anaerobic zone to promote EBPR. Two trains of the activated sludge system at the Des Moines, Iowa Metropolitan Wastewater Reclamation Facility were used for the study with one train modified for EBPR, and the other remained as nitrification-only for comparison.In addition to measuring the modification effectiveness for phosphorus removal, performance was compared during dry and wet weather conditions over the course of two summer seasons to improve understanding of wet and dry weather dynamics for EBPR. DNA sequencing and qPCR tests were conducted to develop an understanding of microbial population changes between control and modified basins and wet and dry weather conditions.Basin hydraulic retention times varied from 2.6 to 12.7 hours with an average of 8.9 hours. EBPR activity was successfully established in the modified basins with average phosphorus content of the return activated sludge 0.032 ± 0.002 compared to 0.016 ± 0.001 mg TP/mg TSS (95% confidence) in the control basins. Phosphorus removal was significantly decreased by prolonged wet weather conditions, particularly in year two of the study, however the modified basin maximum removal of 96% and average of 43.7 ± 5.3% remained significantly higher than the maximum of 46% and average 12.6 ± 2.4% removal in the control basins.DNA sequencing showed a significant increase in relative abundance of phyla Chloroflexi, Nitrospirae, and Verrucomicrobia in the modified basins, but no correlation to EBPR performance. qPCR indicated significant increase in relative quantity of Accumulibacter, but not for Actinetobacter-like phosphorus accumulating organisms (PAOs), which includes the PAO Tetrasphaera. Significant abundance of some Accumulibacter clades found within the modified basins was contrary to previous literature which focused on small-scale and batch studies. A higher than expected dominance of clade I and increased relative quantities of clades IIB and IIC during extended wet weather was observed which may have contributed to rapid recovery of phosphorus removal when dry weather resumed. The abundance of PAOs did not significantly correlate with changes in phosphorous removal performance, contrary to reports from previous small-scale and batch studies.

Metagenomic analysis of bacterial communities of Wadi Namar Lake, Riyadh, Saudi Arabia

Wadi Namar lake is a new touristic attraction area in the south of Riyadh. Human activities around the lake may lead to changes in water quality with subsequent changes in microenvironment components including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water at Wadi Namar Lake. Therefore, water samples were collected from three different locations along the lake: L1 (no human activities, no plants), L2 (no human activity, some plants) and L3 (human activities, municipal wastes and some plants). The total DNA of the samples was extracted and subjected to 16S rDNA sequencing and metagenomic analysis; water pH, electrical conductivity (EC), total dissolved solids (TDS) as well as the concentration of Na+1, K+1, Cl−1 and total N were analysed. Metagenomic analysis showed variations in relative abundance of 17 phyla, 31 families, 43 genera and 19 species of bacteria between the locations. Proteobacteria was the most abundant phylum in all locations; however, its highest abundance was in L1. Planctomycete phylum was highly abundant in L1 and L3, while its abundance in L2 was low. The phyla Acidobacteria, Candidatus Saccharibacteria, Nitrospirae and Chloroflexi were associated with high TDS, EC, K+1 and Cl−1 concentrations in L3; various human activities around this location had possibly affected microbial diversity. Current study results help in recognising the structure of bacterial communities at Wadi Namar Lake in relation to their surroundings for planning to environment protection and future restoration of affected ecosystems.

The molecular characteristics of dissolved organic matter in urbanized river sediments and their environmental impact under the action of microorganisms

The complex relationships between the molecular composition of dissolved organic matter (DOM) and microbial communities are essential for maintaining the stability of aquatic ecosystems. This study comprehensively analyzed the characteristics and potential effects of DOM molecular composition as well as the relationship between microbial communities and DOM molecular composition in sediments from the Beiyun River, Beijing, China. The results showed that the content of DOM in Beiyun River sediments was 9.93–41.57 g/kg, mainly composed of lignin-like (36.75%) and protein-like (17.79%) substances. Compared with other rivers affected by anthropogenic activities, the higher content of labile substances in the Beiyun River increased the risk of nutrient release. At the same time, 1402 molecules remained stable in each sample, most of which were refractory lignin-like substances and protein-like substances carrying ester groups. The agricultural section contained more common DOM molecules than the urban section, mainly tannin-like and lignin-like substances with unsaturated or cyclic structures. And, the intensity of anthropogenic activities was the main reason affecting the diversity of unique DOM molecular in each sample. Moreover, Dechloromonas as the dominant genus of Proteobacteria was closely related to the biological modification of low unsaturated (DBE < 15) condensed aromatic compounds (P < 0.05). Anaerolineaceae and Anaerolineae belonging to the Chloroflexi phylum have the potential to degrade medium and high molecular weight (M/Z > 400) liable substances (P < 0.05) and release lignin-like substances. In addition, the proportion of protein-like substances can indirectly reflect the risk of nutrient release in sediments affected by urbanization. Thus, the results of this study further reveal the impact of urbanization on rivers, and provide theoretical basis and guidance for pollution control of the Beiyun River and other urbanized rivers worldwide.

English

Mulching has been used widely to improve the production capacity of the soil, yield and the quality of wine grapes (Vitis vinifera L. cv. Cabernet Sauvignon). However, the ecological mechanisms underlying the mulching materials were not well understood. This study aimed to evaluate the effects of different mulching materials on soil chemical properties, bacterial community and wine grape quality. Experiments were performed at a grape-yard on the six-year-old wine grape ‘Vitis vinifera L. cv. Cabernet sauvignon. Five kinds of mulching materials include living turfgrass (Grass), living Herba portulacae (Por), inorganic plastic black film (Film), organic chips of wood (Wood), and grape branches (Branch) were applied, while clean tillage (CK) was treated as a control. Soil chemical properties and grape quality indicators were measured. Soil bacterial community diversity was detected using the Illumina Miseq sequencing for the 16S rRNA gene V3-V4 region. Mulching with plastic film, wood chips and Herba portulacae (Por) increased the content of soil organic matter, available N, P and K, total N and P. Film, grass, branch and Por mulching materials improved the content of tannin, anthocyanin, total phenol and titratable acid in grape (p&lt;0.05). Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were abundant bacteria. Mulching with grape branch and portulacae increased the relative abundance of Gemmatimonadetes and Chloroflexi phylum, Gemmatimonadaceae family, and decreased Micrococcaceae family and Pseudarthrobacter genus. Mulching with living, organic, or inorganic changed chemical properties and grape quality indicators. These changes might be correlated with the altered soil bacterial community diversity and richness. © 2022 Friends Science Publishers

The shifts in the structure of the prokaryotic community of mountain-grassland soil under the influence of artificial larch plantations.

Creation of artificial forest plantations on a global scale is one of the ways to mitigate the negative effects of climate change on ecosystems, at the same time providing soil protection from erosion, regulation of the hydrological regime and carbon sequestration in soils of different natural and climatic zones. However, the change of the dominant plant community cause significant ecosystem changes, reflecting at the structure and functioning of the soil microbial complex as well. The shifts in prokaryotic community of the meadow soil resulting from the conversion of the native meadow (further grassland) phytocenosis to the artificial forest plantations was investigated with the use of NGS sequencing technology and metabarcoding approach–amplicon sequencing of V4 region of 16 S rRNA (performed on Illumina Miseq platform). The identified shifts in taxonomic structure and diversity may be the result of changes in the physic-chemical conditions of soils and, on the other hand, may serve as indicators of such changes. Cultivation of larch led to an increase in the diversity of the prokaryotic community and its stratification by depth. The acidifying effect of larch manifested itself in an increase in the proportion and diversity of acidobacteria, in the abundance of oligotrophic microorganisms of phyla Chloroflexi, Firmicutes, and a simultaneous comparative decrease in the bacteria of Verrucomicrobia phylum, alphaproteobacteria of or. Rhizobiales and Burkholderiales. The absence of clearly expressed dominants in the prokaryotic community, as well as a significant increase in alpha-diversity indices, compared with the control plot of native mountain-meadow soil under grassland vegetation, suggests a transitional nature of the soil ecosystem of artificial forest plantations.

Superphosphate, biochar, and a microbial inoculum regulate phytotoxicity and humification during chicken manure composting

The germination index (GI) is the best index for evaluating compost phytotoxicity and maturity. In order to improve GI and reduce phytotoxicity of chicken manure compost, superphosphate, biochar, and a microbial inoculum were added in this study. Maturity indices (pH, electrical conductivity, and GI), water-soluble ion, organic matter, humic acid, humic precursor contents, and the bacteria community were analyzed during the experiment. NH4+, volatile fatty acids, and humic acid strongly affected the GI, which increased as the humic acid content increased and the volatile fatty acid and NH4+ contents decreased. The three additives affected compost maturity differently. Adding biochar decreased microbial diversity and complexity, but improved the GI mainly by affecting abiotic factors. Adding the microbial inoculum increased biotic activity and promoted humus and precursor formation. Superphosphate activated core functional bacteria and increased bacterial diversity and complexity, and 16 genera and 2 phyla (Gemmatimonadota and Chloroflexi) were found only in this composting pile. Superphosphate markedly accelerated humification and decreased the salt (NH4+ and NO3−) and heavy metal ion (Cu2+, Cd2+, Cr3+) contents, forming stable substances to reduce the key phytotoxic matters, which in turn decreased the compost phytotoxicity and improved the GI. These results provide a new sight for promoting maturity by functional material regulation in composting.

Long-term land use in Amazon influence the dynamic of microbial communities in soil and rhizosphere

Brazil has become the world leader in soy production, leading to an increase in the conversion of the Amazon rainforest into cropland. These actions had consequences for Forest's biodiversity, including the soil. In this sense, a better understanding of how long-term land use affects soil microbial communities, and their functions is urgent. This study aimed to evaluate the long-term land-use effects over bacterial and archaeal communities in soil and soybean rhizosphere in the Amazon region. For this, mesocosms experiments were carried out with Amazon soils with a history of 2-, 8-, and 20-years of agricultural use. We then assessed the bacterial and archaeal communities based on the 16S rRNA sequencing and real-time PCR. Our results showed a distinct bacterial community structure in soils with 20-years of land use. For both, bulk soil and soybean rhizosphere with 20-years of use, there was an increase in the abundance of Gemmatimonadetes, Chloroflexi, Firmicutes, and Planctomycetes. Interestingly, the niche occupancy analysis revealed an increase of specialist microbes in these soils. Also, these soils with 20-years of use showed a more complex network for both bulk and rhizosphere samples, highlighting the importance of Actinobacteria and Chloroflexi phyla to soil network structure. Our analysis also revealed an increased abundance of total bacteria, N-fixers, and ammonia-oxidizers bacteria in rhizosphere soil with 20-years of use. In addition, based on the potential functional analysis, nitrification processes increased in those soils. However, we noticed a homogenization in the abundance of the genes between rhizosphere and bulk soil with 20-years of use. In general, the differences were associated with changes in soil chemical characteristics such as pH, Ca2+, Mg2+, and organic matter, which are a consequence of liming and no-till practices over time. Our findings demonstrate that long-term agriculture in Amazon soils affects microbial community composition and functions, bringing new insights to better understand anthropogenic actions over the soil microbiome.