Profiling gene expression to distinguish the likely active diazotrophs from a sea of genetic potential in marine sediments

Abstract

Nitrogen (N) cycling microbial communities in marine sediments are extremely diverse, and it is unknown whether this diversity reflects extensive functional redundancy. Sedimentary denitrifiers remove significant amounts of N from the coastal ocean and diazotrophs are typically regarded as inconsequential. Recently, N fixation has been shown to be a potentially important source of N in estuarine and continental shelf sediments. Analysis of expressed genes for nitrite reductase (nirS) and a nitrogenase subunit (nifH) was used to identify the likely active denitrifiers and nitrogen fixers in surface sediments from different seasons in Narragansett Bay (Rhode Island, USA). The overall diversity of diazotrophs expressing nifH decreased along the estuarine gradient from the estuarine head to an offshore continental shelf site. Two groups of sequences related to anaerobic sulphur/iron reducers and sulphate reducers dominated libraries of expressed nifH genes. Quantitative polymerase chain reaction (qPCR) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) data shows the highest abundance of both groups at a mid bay site, and the highest nifH expression at the head of the estuary, regardless of season. Several potential environmental factors, including water temperature, oxygen concentration and metal contamination, may influence the abundance and nifH expression of these two bacterial groups.

Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling

“…Our study shows that the major nifH phylotypes in seagrass sediments, SL1 of Fe(III)-reducing bacteria and SL2 of Desulfobulbaceae SRB, actually represent the same groups called NB3 and NB7, respectively, elsewhere (43,44). The NifH amino acid sequences of the Desulfobulbus-related SL4 translated from the nifH sequence form a lineage different from the NB10 group (data not shown), a minor group related to Desulfovibrio (44).…”

“…Furthermore, cyanobacterial 16S rRNA genes were found to be rare in our Ion Torrent sequencing data set, representing only 0.1 to 0.5% of the sequences in the sets of sequences representing the entire bacterial communities; most of these cyanobacteria were also affiliated with nondiazotrophic Synechococcus in our samples. In fact, cyanobacterial nifH sequences were not detected in the sediments of Narragansett Bay, even though primers whose sequences matched the nifH sequences of most cyanobacteria were applied for PCR amplification (44). These findings indicate that nitrogen-fixing cyanobacteria were very likely not present or were minor members of the diazotrophic communities in these coastal sediments.…”

“…Recent studies of the diazotrophic diversity in bare coastal sediments revealed two main nifH groups which appeared to be phylogenetically related to Pelobacter and Desulfovibrio and were named NB3 and NB7, respectively (43,44). To explore their phylogenetic relationships with our major OTUs (e.g., SL1, SL2, and SL4), we performed ML analyses of the NifH protein sequences of NB3 and NB7 translated from the nifH sequences together with our sequences.…”

“…It has been reported that the nifH gene abundance ranges from 1.0 ϫ 10 6 to 6.0 ϫ 10 8 copies g Ϫ1 sediment in several marine benthic habitats (44,53,54). Our data on nifH gene abundance in the shallow seagrass system are consistent with those reported for a Brazilian mangrove (53), a subtropical coastal lagoon (54), and the Narragansett Bay and the southern coast of Rhode Island and Massachusetts (44), but the nifH gene abundance that we found is higher than that from deep-sea sites in the northern South China Sea (55), suggesting a spatial gradient of benthic N 2 fixation potential from shallow, plant-dwelling coastal systems to deep oceans.…”

Significant N2 fixation by heterotrophs, photoheterotrophs and heterocystous cyanobacteria in two temperate estuaries

“…Taken together with the recent reports of significant N 2 fixation in estuarine sediments (Fulweiler et al, 2013;Brown and Jenkins, 2014), the basin-scale implications of estuarine N 2 fixation are likely considerable, suggesting that a reevaluation of the significance of N 2 fixation in temperate estuaries and coastal waters is warranted. Moreover, the N 2 fixation by heterotrophic, photoheterotrophic and heterocystous bacteria suggested from the present study highlights the importance of integrating all these three fundamentally different groups in future surveys of estuarine diazotrophy.…”