Diversity and Detection of Nitrate Assimilation Genes in Marine Bacteria

Allen, Andrew E.; Booth, Melissa G.; Frischer, Marc E.; Verity, Peter G.; Zehr, Jonathan P.; Zani, Sabino

doi:10.1128/aem.67.11.5343-5348.2001

Cited by 111 publications

(89 citation statements)

References 53 publications

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“…In a study of coral mucus additions to seawater (Allers et al, 2008), a rapid increase in the abundance of Alteromonas bacteria concomitant with significant decreases in the C:N ratio of particulate organic matter was found, suggesting that they rapidly assimilated dissolved organic carbon. Marinobacter is the most common heterotrophic organism associated with libraries of the assimilatory nitrate uptake gene nasB in nitraterich waters (Allen et al, 2001). Trichodesmium is known to exude fixed N and C into surrounding waters (Capone et al, 1994;Mulholland et al, 2006).…”

Section: Metatranscriptome Library Characteristicsmentioning

confidence: 99%

Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean

et al. 2009

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Trichodesmium are responsible for a large fraction of open ocean nitrogen fixation, and are often found in complex consortia of other microorganisms, including viruses, prokaryotes, microbial eukaryotes and metazoa. We applied a community gene expression (metatranscriptomic) approach to study the patterns of microbial gene utilization within colonies of Trichodesmium collected during a bloom in the Southwest Pacific Ocean in April 2007. The survey generated 5711-day and 5385-night putative mRNA reads. The majority of mRNAs were from the co-occurring microorganisms and not Trichodesmium, including other cyanobacteria, heterotrophic bacteria, eukaryotes and phage. Most transcripts did not share homology with proteins from cultivated microorganisms, but were similar to shotgun sequences and unannotated proteins from open ocean metagenomic surveys. Trichodesmium transcripts were mostly expressed photosynthesis, N 2 fixation and S-metabolism genes, whereas those in the co-occurring microorganisms were mostly involved in genetic information storage and processing. Detection of Trichodesmium genes involved in P uptake and As detoxification suggest that local enrichment of N through N 2 fixation may lead to a P-stress response. Although containing similar dominant transcripts to open ocean metatranscriptomes, the overall pattern of gene expression in Trichodesmium colonies was distinct from free-living pelagic assemblages. The identifiable genes expressed by Trichodesmium and closely associated microorganisms reflect the constraints of life in well-lit and nutrient-poor waters, with biosynthetic investment in nutrient acquisition and cell maintenance, which is in contrast to gene transcription by soil and coastal seawater microbial assemblages. The results provide insight into aggregate microbial communities in contrast to planktonic free-living assemblages that are the focus of other studies. The ISME Journal (

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Section: Metatranscriptome Library Characteristicsmentioning

confidence: 99%

Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean

et al. 2009

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“…The universal bacterial primers 27F (5 0 -AGAGTTTGATCCTGGCTCAG-3 0 ) and 1492R (5 0 -GGTTACCTTGTTACGACTT-3 0 ) were used to amplify community DNA. The nitrate assimilation gene nasA was amplified using the primers nas964 and nasA1735 [15] and newly designed primer set: nasF30 (5 0 -TAYTGYGGBGTNGGNTG-3 0 ) and nasR1080 (5 0 -CCCATNGCRTTNGGYTG-3 0 ) in this study, with the following cycling conditions: 95°C for 4 min, followed by 30 cycles, 95°C for 50 s, 30 s at 53°C, 50 s at 72°C, with a 7 min final extension. The PCR products were gel-purified and ligated into pMD18-T vectors, then transformed into Escherichia coli DH5a competent cells (TaKaRa, Dalian, China).…”

Section: Sample Collectionmentioning

confidence: 99%

“…The concentration of nitrate was high in the deep ocean. The spacial distribution of nitrate-assimilating bacteria (NAB) has been investigated using the nasA gene in various oceanic surface waters [15][16][17]. However, these studies were not emphasized on the difference of NAB in the vertical dimension.…”

Section: Introductionmentioning

confidence: 99%

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Vertical Distribution of Bacterial Communities in the Indian Ocean as Revealed by Analyses of 16S rRNA and nasA Genes

Jiang

Jiao

2016

Indian J Microbiol

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Bacteria play an important role in the marine biogeochemical cycles. However, research on the bacterial community structure of the Indian Ocean is scarce, particularly within the vertical dimension. In this study, we investigated the bacterial diversity of the pelagic, mesopelagic and bathypelagic zones of the southwestern Indian Ocean (50.46°E, 37.71°S). The clone libraries constructed by 16S rRNA gene sequence revealed that most phylotypes retrieved from the Indian Ocean were highly divergent from those retrieved from other oceans. Vertical differences were observed based on the analysis of natural bacterial community populations derived from the 16S rRNA gene sequences. Based on the analysis of the nasA gene sequences from GenBank database, a pair of general primers was developed and used to amplify the bacterial nitrate-assimilating populations. Environmental factors play an important role in mediating the bacterial communities in the Indian Ocean revealed by canonical correlation analysis.

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“…Res., 9 (5): 223-236, 2015 Bacterial Genomic DNA extraction kit (Bio Basic, Canada) according to the manufacturer's instruction. The partial DNA fragment of bacterial 16S rRNA gene was amplified by PCR using a forward primer fd1 (5'-AGAGTTTGATCCTGGCTCAG-3') and a reverse primer rp2 (5'-ACGGCTACCTTGTTACGACTT-3') (Allen et al, 2001). For the ITS region, the highly conserved sequences were designed based on published sequences with adjacent 3' end region of the 16S rRNA and 5' end region of the 23S rDNA using a forward primer ITS-16SF (5'-CGGTGAATACGTTCCCGGGYCTTG-3') and a reverse primer ITS-23SR (5'-TTTCRCCTTTCCCTCACGGTA-3').…”

Section: Amplification Of 16s Rrna and Internal Transcribed Region (Imentioning

confidence: 99%

Elucidating the Probiotic Potential of Malaysian Paenibacillus pabuli Against Vibrio alginolyticus in Artemia Culture

Ina-Salwan¹,

Hishammudd²,

Zulperi³

et al. 2015

Asian J. of Agricultural Research

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In the present study, two strains of Malaysian Paenibacillus spp. isolated from intestinal tract of cultured hybrid red tilapia were tested for their antagonistic activity against Vibrio alginolyticus, a destructive bacterial pathogen to marine fishes as probiotics in aquaculture. Homology searches of 16S rRNA and Internal Transcribes Spacer (ITS) genes sequencing with nucleotide Basic Local Alignment Sequence Tool (nBLAST) revealed that both strains were identical to Paenibacillus spp. and Paenibacillus pabuli, respectively. In vitro and in vivo experiments were conducted to study the efficacy of these Paenibacillus strains as probiotics. Co-culture assay demonstrated that the growth of V. alginolyticus was inhibited when grown with these probionts. A complete inhibition of the pathogen by P. pabuli strain D12 occurred at 48 h of incubation period. To qualify strains as probiotics, Artemia challenged with V. alginolyticus was performed, with or without these potential probiotics. The highest survival rate (72%) of Artemia was observed in P. pabuli strain D12 treatment after challenged with V. alginolyticus, followed by P. pabuli strain D14 at 68% survival rate. The lowest survival of Artemia (23% survival rate) was recorded when challenged with only V. alginolyticus. This study reported the ability of Paenibacillus D12 and D14 as potential probiotics to control V. alginolyticus in Artemia culture system.

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Diversity and Detection of Nitrate Assimilation Genes in Marine Bacteria

Cited by 111 publications

References 53 publications

Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean

Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean

Vertical Distribution of Bacterial Communities in the Indian Ocean as Revealed by Analyses of 16S rRNA and nasA Genes

Elucidating the Probiotic Potential of Malaysian Paenibacillus pabuli Against Vibrio alginolyticus in Artemia Culture

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