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

Yousuf, Basit; Kumar, Raghawendra; Mishra, Avinash; Jha, Bhavanath

doi:10.1111/1574-6968.12593

Cited by 42 publications

(18 citation statements)

References 57 publications

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“…The total copy numbers of these Klebsiella- and Clostridiales-related nifH genes were 10 5 –10 9 copies per gram wet faeces (Table 4) and not correlated with the host nitrogen intake (Table 1) or with the nitrogen-fixing activity (Table 2). These nifH copy numbers are comparable to those in other diazotrophic environments, such as corals (10 7 copies per gram tissue)7 and the rhizosphere (10 5 –10 7 copies per gram soil)3940.…”

Section: Discussionsupporting

confidence: 68%

Nitrogen fixation and nifH diversity in human gut microbiota

Igai

Itakura

Nishijima

et al. 2016

Sci Rep

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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.

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Section: Discussionsupporting

confidence: 68%

Nitrogen fixation and nifH diversity in human gut microbiota

Igai

Itakura

Nishijima

et al. 2016

Sci Rep

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“…Although the total numbers of the major genera were not changed, but the relative percentages of the genera were altered by DMP contamination (Figure 1 ). Azohydromonas and Microvirga are key players in the nitrogen cycle in soils (Coelho et al, 2008 ; Ardley, 2012 ; Yousuf et al, 2014 ), and the relative percentages of Azohydromonas increased along with the increase in DMP concentration. The relative percentages of Microvirga increased along with the increase in lower DMP concentration, but dropped in the highest DMP concentration.…”

Section: Discussionmentioning

confidence: 99%

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

Wang

et al. 2015

Front. Microbiol.

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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.

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“…The 16S rRNA gene was amplified using genomic DNA and universal bacterial primers ( Table 1 ). The 50 μL PCR mixture was contained; 1–2 μL DNA template, 0.5 μL 20 μM of each primer, 5 μL of 10X buffer, 5 μL of dNTPs (2.5 mM), 0.5 μL Taq DNA (5 units/μL), and 41.5 mL ddH 2 O. PCR was done in MyCyclerT-100 (Bio-Rad, United States) using the optimized conditions ( Yousuf et al, 2012 , 2014a , b ; Keshri et al, 2013 ; Keshri et al, 2015 ). The amplified products were analyzed on a 1.0% agarose gel, purified (QIAquick PCR Purification Kit, Qiagen, Germany) and sent to M/s Macrogen, S. Korea for the sequencing services.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2017

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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.

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

Cited by 42 publications

References 57 publications

Nitrogen fixation and nifH diversity in human gut microbiota

Nitrogen fixation and nifH diversity in human gut microbiota

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

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

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