Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach

Application of microbial resources in biorefineries: Current trend and future prospects

The recent growing interest in sustainable and alternative sources of energy and bio-based products has driven the paradigm shift to an integrated model termed "biorefinery." Biorefinery framework implements the concepts of novel eco-technologies and eco-efficient processes for the sustainable production of energy and value-added biomolecules. The utilization of microbial resources for the production of various value-added products has been documented in the literatures. However, the appointment of these microbial resources in integrated resource management requires a better understanding of their status. The main of aim of this review is to provide an overview on the defined positioning and overall contribution of the microbial resources, i.e., algae, fungi and bacteria, for various bioprocesses and generation of multiple products from a single biorefinery. By utilizing waste material as a feedstock, biofuels can be generated by microalgae while sequestering environmental carbon and producing value added compounds as by-products. In parallel, fungal biorefineries are prolific producers of lignocellulose degrading enzymes along with pharmaceutically important novel products. Conversely, bacterial biorefineries emerge as a preferred platform for the transformation of standard cells into proficient bio-factories, developing chassis and turbo cells for enhanced target compound production. This comprehensive review is poised to offer an intricate exploration of the current trends, obstacles, and prospective pathways of microbial biorefineries, for the development of future biorefineries.

Recovery mechanism of bio-promoters on Cr(VI) suppressed denitrification: Toxicity remediation and enhanced electron transmission

Although the biotoxicity of heavy metals has been widely studied, there are few reports on the recovery strategy of the inhibited bio-system. This study proposed a combined promoter-I (Primary promoter: l-cysteine, biotin, and cytokinin + Electron-shuttle: PMo12) to recover the denitrification suppressed by Cr(VI). Compared with self-recovery, combined promoter-I shortened the recovery time of 28 cycles, and the recovered reactor possessed more stable long-term operation performance with >95 % nitrogen removal. The biomass increased by 7.07 mg VSS/(cm3 carrier) than self-recovery due to the promoted bacterial reproduction, thereby reducing the toxicity load of chromium per unit biomass. The combined promoter-I strengthened the toxicity remediation by promoting 92.84 % of the intracellular chromium release and rapidly activating anti-oxidative stress response. During toxicity remediation, ROS content quickly decreased, and the PN/PS value was 2.27 times that of self-recovery. PMo12 relieved Cr(VI) inhibition on NO3--N reduction by increasing NAR activity. The enhanced intracellular and intercellular electron transmission benefited from the stimulated NADH, FMN, and Cyt.c secretion by the primary promoter and the improved transmembrane electron transmission by Mo. PMo12 and the primary promoter synergized in regulating community structure and improving microbial richness. This study provided practical approaches for microbial toxicity remediation and maintaining high-efficiency denitrification.

Organic management increases beneficial microorganisms and promotes the stability of microecological networks in tea plantation soil

Introduction

Organic agriculture is highly regarded by people for its commitment to health, ecology, care, and fairness. The soil microbial community responds quickly to environmental changes and is a good indicator for evaluating soil microecology. Therefore, from the perspective of soil microbial communities, elucidating the impact of organic management on soil microecology in tea plantations has great significance for improving local tea plantation systems.

Methods

The study collected bulk soil from organic management (OM) and conventional management (CM) tea plantations in Pu'er City, a major tea-producing area in China, and analyzed their species diversity, structural composition, and co-occurrence networks using metagenomics technology.

Results

Compared with CM, the diversity index (Shannon) and evenness index (Heip) of soil fungi increased by 7.38% and 84.2% in OM tea plantations, respectively. The relative abundance of microorganisms related to the nitrogen cycle increased. Specifically, there was a significant increase in Rhodobiales, a 2-fold increase in Nitrospirae, and approximately 1.95 and 2.03 times increases in unclassified genera within Betaproteobacteria and Deltaproteobacteria, respectively. The relative abundance of plant residue degradation species, Gemmatimonadetes, Ascomycota, and Basidiomycota, increased by 2.8, 1, and 1.4 times, respectively. The OM was conducive to the establishment of collaborative relationships among bacterial species and increased the diversity and complexity of species relationships in fungal communities. The network stability of soil ecosystems was promoted. The organic tea plantations' keystone taxa contained mycorrhizal fungi (Pezoloma_ericae, Rhizophagus_irregularis, Rhizophagus_clarus), as well as species involved in soil nitrogen metabolism (Acidobacteria_bacterium, Acidobacteriia_bacterium_AA117, Sphingomonas_sp._URHD0007, Enhydrobacter_aerosaccus), pathogen (Erysiphe_pulchra), and parasites (Paramycosporidium saccamoeba). The partial least squares method (PLS-SEM) indicated that OM affected N-NH4 + negatively, increasing the abundance of fungi, and thereby positively affecting the Shannon index.

Conclusion

In brief, reasonable organic management can improve the diversity of soil microorganisms, increase the relative abundance of beneficial bacteria in tea plantation soil, and promote the stability of the soil microbial ecological network.

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

Introduction

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.

Methods

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.

Results and Discussion

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.

Sugarcane Rhizosphere Bacteria Community Migration Correlates with Growth Stages and Soil Nutrient

Plants and rhizosphere bacterial microbiota have intimate relationships. As neighbors of the plant root system, rhizosphere microorganisms have a crucial impact on plant growth and health. In this study, we sampled rhizosphere soil of sugarcane in May (seedling), July (tillering), September (elongation) and November (maturity), respectively. We employ 16S rRNA amplicon sequencing to investigate seasonal variations in rhizosphere bacteria community structure and abundance, as well as their association with soil edaphic factors. The results demonstrate that soil pH, total nitrogen (TN) and available nitrogen (AN) decrease substantially with time. Rhizosphere bacteria diversity (Shannon) and the total enriched OTUs are also significantly higher in July relative to other months. Bacteria OTUs and functional composition exhibit a strong and significant correlation with soil temperature (Tem), suggesting that Tem was the potential determinant controlling rhizosphere bacteria diversity, enriched OTUs as well as functional composition. Redundancy analysis (RDA) point toward soil total potassium (TK), pH, TN, Tem and AN as principal determinant altering shifting bacteria community structure. Variation partitioning analysis (VPA) analysis further validate that a substantial proportion of variation (70.79%) detected in the rhizosphere bacteria community structure was attributed to edaphic factors. Mfuzz analysis classified the bacterial genera into four distinct clusters, with cluster two exhibiting a distinct and dramatic increase in July, predominantly occupied by Allocatelliglobosispora. The stochastic forest model found the key characteristic bacterial populations that can distinguish the four key growth periods of sugarcane. It may help us to answer some pending questions about the interaction of rhizosphere microorganisms with plants in the future.

The phylogeny of the genus Azohydromonas supports its transfer to the family Comamonadaceae

The genus Azohydromonas encompasses five validly described species belonging to the betaproteobacterial class. Recognized for their potential biotechnological uses, they were first described as belonging to the genus Alcaligenes. The phylogeny of the 16S rRNA gene of the original strains as well as newly described species led to a description of these strains within a new bacterial genus, Azohydromonas. However, the phylogenetic position of this genus remains described as part of the family Alcaligenaceae, even those some authors have placed it within the order Burkholderiales. To unravel the precise position of the genus Azohydromonas, a wide phylogenomic analysis was performed. The results of 16S rRNA gene phylogeny, as well as those obtained by the multilocus analysis of homologous proteins and overall genome relatedness indices, support the reclassification of Azohydromonas in the Rubrivivax-Ideonella lineage of the family Comamonadaceae, so the transfer of this genus is proposed.

Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses

Mangroves are highly productive unique ecosystems harboring diverse unexplored microbial communities that play crucial roles in nutrient cycling as well as in maintaining ecosystem services. The mangrove-associated microbial communities transform the dead vegetation into nutrient sources of nitrogen, phosphorus, potash, etc. To understand the genetic and functional diversity of the bacterial communities involved in nitrogen cycling of this ecosystem, this study explored the diversity and distribution of both the nitrogen fixers and denitrifiers associated with the rhizospheres of Avicennia marina, Rhizophora mucronata, Suaeda maritima, and Salicornia brachiata of the Pichavaram mangroves. A combination of both culturable and unculturable (PCR-DGGE) approaches was adopted to explore the bacterial communities involved in nitrogen fixation by targeting the nifH genes, and the denitrifiers were explored by targeting the nirS and nosZ genes. Across the rhizospheres, Gammaproteobacteria was found to be predominant representing both nitrogen fixers and denitrifiers as revealed by culturable and unculturable analyses. Sequence analysis of soil nifH, nirS and nosZ genes clustered to unculturable, with few groups clustering with culturable groups, viz., Pseudomonas sp. and Halomonas sp. A total of 16 different culturable genera were isolated and characterized in this study. Other phyla like Firmicutes and Actinobacteria were also observed. The PCR-DGGE analysis also revealed the presence of 29 novel nifH sequences that were not reported earlier. Thus, the mangrove ecosystems serve as potential source for identifying unexplored novel microbial communities that contribute to nutrient cycling.

Long-term organic and inorganic fertilization alters the diazotrophic abundance, community structure, and co-occurrence patterns in a vertisol

Diazotrophs play a critical role in converting air-inactive nitrogen to bio-available nitrogen. Assessing the influences of different fertilization regimes on diazotrophs is essential for a better understanding of their maintenance of soil fertility and agricultural sustainability. In this study, we targeted the nifH gene to investigate the effects of different long-term fertilization on the diazotrophic community in a vertisol, using real-time quantitative polymerase chain reaction (PCR) and MiSeq sequencing. Five fertilization regimes were tested: no fertilizer (CK), chemical nitrogen, phosphorus, and potassium fertilizer (NPK), organic fertilizer (O), chemical NPK plus organic fertilizer with an equivalent application rate of nitrogen (NPKO), and chemical NPK plus organic fertilizer with a high application rate of nitrogen (HNPKO). Our results showed that fertilization significantly affected the diazotrophic activity, abundance and composition. NPK tended to reduce the activity, abundance, operational taxonomic units (OTU)-richness and alpha-diversity of the diazotrophs, while O had the opposite effect. The effects of inorganic and organic fertilization on the diazotrophs depended on the N application rate, showing that the diazotrophic activity, abundance, and alpha-diversity in NPKO were higher than that of HNPKO. For the diazotrophic community structure, CK, O, and NPKO were grouped and separated from NPK and HNPKO. The diazotrophic community structure strongly correlated with the soil pH, electrical conductivity (EC), total carbon content (TC), and total nitrogen content (TN), among which pH was the major factor shaping the diazotrophic community structure. Different network patterns were observed between the long-term organic and non-organic fertilizers, suggesting that the organic amendment resulted in a more complicated diazotrophic community than the non-organic amendments. Rhizobium was the most important hub connecting members in the community. These results indicated that organic amendments are beneficial to diazotrophic activity, abundance, OTU richness, alpha-diversity, and the diazotrophic communities' potential interactions, which may enhance biological nitrogen fixation in vertisols.

Assessment of Diazotrophic Proteobacteria in Sugarcane Rhizosphere When Intercropped With Legumes (Peanut and Soybean) in the Field

Several factors influenced the sugarcane production, and among them, higher use of nitrogen and depletion of soil nutrient constitutes a significant concern in China. Sugarcane-legume intercropping may help to regulate the microbial structure and functions. In the present study, sugarcane rhizosphere soils of three cropping systems: Sugarcane only (S-only), sugarcane with peanut (S + P), and sugarcane + soybean (S + S) were sampled in tillering, elongation, and maturation stages from two different experimental fields. High-throughput sequencing technologies applied to assess the effects of different cropping systems on the structure of nitrogenase (nifH) gene communities. A total of 3818 OTUs (operational taxonomic units) were acquired from all soil samples. Intercropping systems noticeably increased the relative abundance of Proteobacteria in the tillering stage. The increased microbial diversity in the rhizosphere was mainly due to soil organic carbon and total soil N. In contrast, intercropping has no significant negative impact on microbial abundance, but sugarcane growth stages influence it significantly, and two bacteria (Bradyrhizobium and Pseudacidovorax) showed significant shift during plant growth. The results provide insight into the microbial structure of Proteobacteria in the sugarcane legume-intercropping field, and how microbial community behaves in different growth stages. It can boost the microbial activity of the soil, and that could be a new strategy to stimulate soil fertility without causing any negative impact on crop production.

Nitrogen fertilizer and Amorpha fruticosa leguminous shrub diversely affect the diazotroph communities in an artificial forage grassland

Soil diazotrophs have been known to be essential in biological nitrogen (N) fixation, which contributes to the sustainability of agricultural ecosystems. However, there remains an inadequacy of research on the effects of different N inputs from N fertilization and from symbiotic N fixation associated with legumes on the diazotroph communities in agricultural ecosystems. Hence, we investigated the variations in diazotroph abundance and community composition as well as the soil properties with different N inputs in the Guimu-1 hybrid elephant grass cultivation on karst soils in China. We conducted six different N treatments: control, Amorpha fruticosa planting at a spacing of 1.5 × 2 m (AFD1), A. fruticosa planting at a spacing of 1 × 2 m (AFD2), N fertilization (N), A. fruticosa planting at a spacing of 1.5 × 2 m with N fertilization (AFD1N), and A. fruticosa planting at a spacing of 1 × 2 m with N fertilization (AFD2N). Our results showed that the interaction between sampling time and N fertilization significantly affected the diazotroph abundance. In July, the diazotroph abundance significantly decreased in the N fertilization treatments: N, AFD1N, and AFD2N, compared to that in the control. The richness and Chao1 estimator of diazotrophs significantly increased in AFD2N and AFD1 correspondingly in December and July, relative to those in the control. Co-occurrence networks showed species-species interactions with high negative correlations that occurred more in the control than in the N input plots. The N input from N fertilization and legume planting directly increased the ammonium N and nitrate N and consequently affected the dissolved organic N and pH of the soil, thereby altering the diazotroph abundance and richness. Our findings demonstrated that both N fertilization and legumes could reduce the interspecific competition among diazotroph species by providing greater N availability in the forage grass.

nifH Gene Sequencing Reveals the Effects of Successive Monoculture on the Soil Diazotrophic Microbial Community in Casuarina equisetifolia Plantations

The growth and productivity of Casuarina equisetifolia is negatively impacted by planting sickness under long-term monoculture regimes. In this study, Illumina MiSeq sequencing targeting nifH genes was used to assess variations in the rhizospheric soil diazotrophic community under long-term monoculture rotations. Principal component analysis and unweighted pair-group method with arithmetic means (UPGMA) clustering demonstrated distinct differences in diazotrophic community structure between uncultivated soil (CK), the first rotation plantation (FCP), the second rotation plantation (SCP), and the third rotation plantation (TCP). Taxonomic analysis showed that the phyla Proteobacteria increased while Verrucomicrobia decreased under the consecutive monoculture (SCP and TCP). The relative abundance of Paraburkholderia, Rhodopseudomonas, Bradyrhizobium, Geobacter, Pseudodesulfovibrio, and Frankia increased significantly while Burkholderia, Rubrivivax, and Chlorobaculum declined significantly at the genus level under consecutive monoculture (SCP and TCP). Redundancy analysis (RDA) showed that Burkholderia, Rubrivivax, and Chlorobaculum were positively correlated with total nitrogen and available nitrogen. In conclusion, continuous C. equisetifolia monoculture could change the structure of diazotrophic microbes in the rhizosphere, resulting in the imbalance of the diazotrophic bacteria population, which might be a crucial factor related to replanting disease in this cultivated tree species.

Plant growth promoting rhizobacterium Stenotrophomonas maltophilia BJ01 augments endurance against N2 starvation by modulating physiology and biochemical activities of Arachis hypogea

Arachis hypogea (Peanut) is one of the most important crops, and it is harvested and used for food and oil production. Being a legume crop, the fixation of atmospheric nitrogen is achieved through symbiotic association. Nitrogen deficiency is one of the major constrains for loss of crop productivity. The bacterium Stenotrophomonas maltophilia is known for interactions with plants. In this study, characteristics that promote plant growth were explored for their ability to enhance the growth of peanut plants under N2 deficit condition. In the presence of S. maltophilia, it was observed that fatty acid composition of peanut plants was influenced and increased contents of omega-7 monounsaturated fatty acid and omega-6 fatty acid (γ-Linolenic acid) were detected. Plant growth was increased in plants co-cultivated with PGPR (Plant Growth Promoting Rhizobacteria) under normal and stress (nitrogen deficient) condition. Electrolyte leakage, lipid peroxidation, and H2O2 content reduced in plants, co-cultivated with PGPR under normal (grown in a media supplemented with N2 source; C+) or stress (nitrogen deficient N+) conditions compared to the corresponding control plants (i.e. not co-cultivated with PGPR; C-or N-). The growth hormone auxin, osmoprotectants (proline, total soluble sugars and total amino acids), total phenolic-compounds and total flavonoid content were enhanced in plants co-cultivated with PGPR. Additionally, antioxidant and free radical scavenging (DPPH, hydroxyl and H2O2) activities were increased in plants that were treated with PGPR under both normal and N2 deficit condition. Overall, these results indicate that plants co-cultivated with PGPR, S. maltophilia, increase plant growth, antioxidant levels, scavenging, and stress tolerance under N2 deficit condition. The beneficial use of bacterium S. maltophilia could be explored further as an efficient PGPR for growing agricultural crops under N2 deficit conditions. However, a detail agronomic study would be prerequisite to confirm its commercial role.

Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests

Amplicon-based analysis of 16S rRNA genes and transcripts was used to assess the effect of tree species composition on soil bacterial community structure and function in a temperate deciduous forest. Samples were collected from mono and mixed stands of Fagus sylvatica (beech), Carpinus betulus (hornbeam), Tilia sp. (lime), and Quercus sp. (oak) in spring, summer, and autumn. Soil bacterial community exhibited similar taxonomic composition at total (DNA-based) and potentially active community (RNA-based) level, with fewer taxa present at active community level. Members of Rhizobiales dominated at both total and active bacterial community level, followed by members of Acidobacteriales, Solibacterales, Rhodospirillales, and Xanthomonadales. Bacterial communities at total and active community level showed a significant positive correlation with tree species identity (mono stands) and to a lesser extent with tree species richness (mixed stands). Approximately 58 and 64% of indicator operational taxonomic units (OTUs) showed significant association with only one mono stand at total and active community level, respectively, indicating a strong impact of tree species on soil bacterial community composition. Soil C/N ratio, pH, and P content similarly exhibited a significant positive correlation with soil bacterial communities, which was attributed to direct and indirect effects of forest stands. Seasonality was the strongest driver of predicted metabolic functions related to C fixation and degradation, and N metabolism. Carbon and nitrogen metabolic processes were significantly abundant in spring, while C degradation gene abundances increased from summer to autumn, corresponding to increased litterfall and decomposition. The results revealed that in a spatially homogenous forest soil, tree species diversity and richness are dominant drivers of structure and composition in soil bacterial communities.

Long-term effect of biochar amendment on the biodegradation of petroleum hydrocarbons in soil microbial fuel cells

Biochar is extensively applied in amendment of contaminated soils. However, the effect of biochar on the biodegradation of petroleum hydrocarbons and electricity generation in soil microbial fuel cells (MFCs) remains unclear. Here, three biochars respectively derived from poultry (chicken manure, CB), agriculture (wheat straw, SB) and forestry industries (wood sawdust, WB) were investigated after 223 days of amendment. Consequently, high removal for alkanes was in CB with the mineral nutrition and phosphorus while aromatics were in SB with the most N content and the highest molecular polarity. The lowest removal efficiency of total petroleum hydrocarbons was observed in WB with the highest surface area, whereas the most charge was obtained. The different performance of soil MFCs was due to physicochemical properties of biochar and colonized microbial communities of bacteria and archaea. The abundance of Actinotalea increased by 144-263% in SB and CB while that of Desulfatitalea distinctly increased in WB. Meanwhile, species from Methanosarcina, Methanoculleus, Halovivax and Natronorubrum exerted probably a methanogenic degrading role. This study revealed that the degrader, azotobacter and electricigens exhibited a close relationship in order to degrade hydrocarbons and generate electricity in soil bioelectrochemical remediation systems.

Antibacterial and Antioxidant Activities of Novel Actinobacteria Strain Isolated from Gulf of Khambhat, Gujarat

Bacterial secondary metabolites possess a wide range of biologically active compounds including antibacterial and antioxidants. In this study, a Gram-positive novel marine Actinobacteria was isolated from sea sediment which showed 84% 16S rRNA gene sequence (KT588655) similarity with Streptomyces variabilis (EU841661) and designated as Streptomyces variabilis RD-5. The genus Streptomyces is considered as a promising source of bioactive secondary metabolites. The isolated novel bacterial strain was characterized by antibacterial characteristics and antioxidant activities. The BIOLOG based analysis suggested that S. variabilis RD-5 utilized a wide range of substrates compared to the reference strain. The result is further supported by statistical analysis such as AWCD (average well color development), heat-map and PCA (principal component analysis). The whole cell fatty acid profiling showed the dominance of iso/anteiso branched C15–C17 long chain fatty acids. The identified strain S. variabilis RD-5 exhibited a broad spectrum of antibacterial activities for the Gram-negative bacteria (Escherichia coli NCIM 2065, Shigella boydii NCIM, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas sp. NCIM 2200 and Salmonella enteritidis NCIM), and Gram-positive bacteria (Bacillus subtilis NCIM 2920 and Staphylococcus aureus MTCC 96). Extract of S. variabilis strain RD-5 showed 82.86 and 89% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging and metal chelating activity, respectively, at 5.0 mg/mL. While H₂O₂ scavenging activity was 74.5% at 0.05 mg/mL concentration. Furthermore, polyketide synthases (PKSs types I and II), an enzyme complex that produces polyketides, the encoding gene(s) detected in the strain RD-5 which may probably involve for the synthesis of antibacterial compound(s). In conclusion, a novel bacterial strain of Actinobacteria, isolated from the unexplored sea sediment of Alang, Gulf of Khambhat (Gujarat), India showed promising antibacterial activities. However, fractionation and further characterization of active compounds from S. variabilis RD-5 are needed for their optimum utilization toward antibacterial purposes.

Bacterial communities associated with anaerobic debromination of decabromodiphenyl ether from mangrove sediment

This study evaluated decabromodiphenyl ether (BDE-209) anaerobic debromination and bacterial community changes in mangrove sediment. BDE-209 debromination rates were enhanced with zerovalent iron compared to without zerovalent iron in the sediment. BDE-209 debromination rates in microcosms constructed with sediments collected in autumn were higher than in microcosms constructed with sediments collected in spring and were higher at the Bali sampling site than the Guandu sampling site. The intermediate products resulting from the reductive debromination of BDE-209 in sediment were nona-BDE (BDE-206, BDE-207), octa-BDEs (BDE-196, BDE-197), hepta-BDEs (BDE-183, BDE-184, BDE-191), hexa-BDEs (BDE-137, BDE-138, BDE-154, BDE-157), penta-BDEs (BDE-85, BDE-99, BDE-100, BDE-126), tetra-BDEs (BDE-47, BDE-49, BDE-66, BDE-77), tri-BDEs (BDE-17, BDE-28), and di-BDEs (BDE-15). Fifty bacterial genera associated with BDE-209 debromination were identified. Overall, 12 of the 50 bacterial genera were reported to be involved in dehalogenation of aromatic compounds. These bacteria have high potential to be BDE-209 debromination bacteria. Different combinations of bacterial community composition exhibit different abilities for BDE-209 anaerobic debromination.

Nitrogen fixation and nifH diversity in human gut microbiota

It has been hypothesized that nitrogen fixation occurs in the human gut. However, whether the gut microbiota truly has this potential remains unclear. We investigated the nitrogen-fixing activity and diversity of the nitrogenase reductase (NifH) genes in the faecal microbiota of humans, focusing on Papua New Guinean and Japanese individuals with low to high habitual nitrogen intake. A ¹⁵N₂ incorporation assay showed significant enrichment of ¹⁵N in all faecal samples, irrespective of the host nitrogen intake, which was also supported by an acetylene reduction assay. The fixed nitrogen corresponded to 0.01% of the standard nitrogen requirement for humans, although our data implied that the contribution in the gut in vivo might be higher than this value. The nifH genes recovered in cloning and metagenomic analyses were classified in two clusters: one comprising sequences almost identical to Klebsiella sequences and the other related to sequences of Clostridiales members. These results are consistent with an analysis of databases of faecal metagenomes from other human populations. Collectively, the human gut microbiota has a potential for nitrogen fixation, which may be attributable to Klebsiella and Clostridiales strains, although no evidence was found that the nitrogen-fixing activity substantially contributes to the host nitrogen balance.

Influence of Vinasse Application in the Structure and Composition of the Bacterial Community of the Soil under Sugarcane Cultivation

Although the use of vinasse as a waste helps replenish soil nutrients and improves the quality of the sugarcane crop, it is known that vinasse residues alter the diversity of bacteria naturally present in the soil. The actual impacts of vinasse application on the selection of bacterial taxa are not understood because no studies have addressed this phenomenon directly. Analysis of 16S rRNA gene clone sequences from four soil types showed that the soil planted with sugarcane and fertilized with vinasse has a high diversity of bacteria compared to other biomes, where Acidobacteria were the second most abundant phylum. Although the composition and structure of bacterial communities differ significantly in the four environments (Libshuff's test), forest soils and soil planted with sugarcane without vinasse fertilizer were similar to each other because they share at least 28 OTUs related to Rhizobiales, which are important agents involved in nitrogen fixation. OTUs belonging to Actinomycetales were detected more often in the soil that had vinasse applied, indicating that these groups are more favored by this type of land management.

Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity

Diazotrophs provide the only biological source of fixed atmospheric nitrogen in the biosphere. Although they are the key player for plant-available nitrogen, less is known about their diversity and potential importance in arid ecosystems. We investigated the nitrogenase gene diversity in native and agricultural desert soil as well as within root-associated microbiota of medicinal plants grown in Egypt through the combination of nifH-specific qPCR, fingerprints, amplicon pyrosequencing and fluorescence in situ hybridization–confocal laser scanning microscopy. Although the diazotrophic microbiota were characterized by generally high abundances and diversity, statistically significant differences were found between both soils, the different microhabitats, and between the investigated plants (Matricaria chamomilla L., Calendula officinalis L. and Solanum distichum Schumach. and Thonn.). We observed a considerable community shift from desert to agriculturally used soil that demonstrated a higher abundance and diversity in the agro-ecosystem. The endorhiza was characterized by lower abundances and only a subset of species when compared to the rhizosphere. While the microbiomes of the Asteraceae were similar and dominated by potential root-nodulating rhizobia acquired primarily from soil, the perennial S. distichum generally formed associations with free-living nitrogen fixers. These results underline the importance of diazotrophs in desert ecosystems and additionally identify plants as important drivers in functional gene pool diversity.

The diazotrophic microbiome of desert ecosystems is characterized by a high diversity and abundance and specific for each plant rhizosphere.

Impacts of dimethyl phthalate on the bacterial community and functions in black soils

Dimethyl phthalate (DMP), a known endocrine disruptor and one of the phthalate esters (PAEs), is a ubiquitous pollutant. Its impacts on living organisms have aroused great concern. In this study, the impacts of DMP contamination on bacterial communities and functions were tested by using microcosm model in black soils. The results showed that the operational taxonomic unit (OTUs) richness and bacterial diversity were reduced by DMP contamination. The relative percentages of some genera associated with nitrogen metabolism were increased by DMP contamination, while the relative percentages of some other genera that were extremely beneficial to soil health were decreased by DMP contamination. Further, the relative percentages of some genera that possessed the capability to degrade DMP were increased by the DMP treatment at low concentrations (5, 10, and 20 mg/kg), but were decreased by the high concentration DMP treatment (40 mg/kg). Clearly, DMP contamination changed the bacterial community structure and disturbed the metabolic activity and functional diversity of the microbes in black soils. Our results suggest that DMP pollution can alter the metabolism and biodiversity of black soil microorganisms, thereby directly impact fertility and ecosystem functions.

The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea

The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further.