Aims:  Shanyin County is one of the most severe endemic arsenism affected areas in China but micro‐organisms that potentially release arsenic from sediments to groundwater have not been studied. Our aim was to identify bacteria with the potential to metabolize or transform arsenic in the sediments. Methods and Results:  Culture and nonculture‐based molecular methods were performed to identify arsenite‐oxidizing bacteria, arsenate‐reducing bacteria and arsenite oxidase genes. Arsenite‐oxidizing bacteria were identified only from the land surface to 7 m underground that were affiliated to α‐ and β‐Proteobacteria. Arsenate‐reducing bacteria were found in almost all the sediment samples with different depths (0–41 m) and mainly belong to γ‐Proteobacteria. Several novel arsenite oxidase genes (aoxBs) were identified from the upper layers of the sediments (0–7 m) and were found to be specific for arsenite‐oxidizing bacteria. Conclusions:  The distribution of arsenite‐oxidizing bacteria in upper layers and arsenate‐reducing bacteria in different depths of the sediments may impact the arsenic release into the nearby tubewell groundwater. Significance and Impact of the Study:  This study provides valuable sources of micro‐organisms (and genes) that may contribute to groundwater arsenic abnormality and may be useful to clean arsenic contaminated groundwater.

We investigated the occurrence and activity of anaerobic ammonia oxidation (anammox) bacteria in sandy and muddy sand sediments of the southern North Sea. The presence of anammox bacteria was established through the detection of specific phosphocholine-monoether ladderane lipids, 16S rRNA gene, and hydrazine synthase (hzsA) genes. Anammox activity was measured in intact sediment cores (in situ rate) and in sediment slurries (potential rate) as the rate of N2 evolution from (15) N-labeled substrates and compared to the transcriptional activity of genes of anammox bacteria. The contribution of anammox to N2 production ranged between 0% and 29%. The potential rate of anammox agreed well with the abundance of anammox bacteria 16S rRNA and hzsA gene copies and the transcriptional activity of the anammox bacteria 16S rRNA gene. We found a higher abundance and activity of anammox bacteria in sediments with higher organic carbon content and also higher activity in summer than in winter. The abundance of anammox bacteria and their potential anammox rates were similar to those reported for other marine coastal sediments, suggesting that potentially they are important contributors to the nitrogen cycle in sandy sediments of shallow continental shelf areas.

We report the draft genome sequence of arsenite-oxidizing Halomonas sp. strain HAL1, isolated from the soil of a gold mine. Genes encoding proteins involved in arsenic resistance and transformation, phosphate utilization and uptake, and betaine biosynthesis were identified. Their identification might help in understanding how arsenic and phosphate metabolism are intertwined. Halomonas sp. strain HAL1, which has a high level of tolerance to arsenite, was isolated from the soil of a gold mine in Daye County, Hubei Province, central China. Strain HAL1 is a heterotrophic, arsenite-oxidizing gammaproteobacterium under aerobic conditions. It is also moderately halophilic and can grow at NaCl concentrations ranging from 0.2 M to 2.0 M in LB, the optimal concentration being 0.8 M. Interest in arsenic and phosphate metabolism in Halomonas was sparked by a recent controversial report claiming that arsenate could replace phosphate in DNA (6, 10). It was therefore desirable to obtain the genomic sequence of a Halomonas strain able to survive in extremely low phosphate concentrations in the presence of arsenic.The genome of Halomonas sp. strain HAL1 was sequenced using a 454 GS FLX sequencer (3) and was assembled using GS de novo assembler ("Newbler"), version 2.5.3. The assembled contigs were submitted to the RAST annotation server for subsystem classification and functional annotation (1). The protein-coding genes (CDSs) were assigned using BLASTp with the KEGG orthology (KO) database. GC content was calculated using an in-house Perl script. The NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP; http://www.ncbi.nlm.nih.gov/genomes /static/Pipeline.html) was employed for gene annotation in preparation for submission to GenBank.The draft genome sequence of Halomonas sp. strain HAL1 comprises 4,347,024 bases at 36-fold coverage. The assembled genome consists of 89 large contigs (Ͼ500 bp) with an average contig size of 102,049 bp and a GϩC content of 54.1%. The draft genome sequence contains 4,082 CDSs, 54 tRNAs, and 8 rRNAs. For the CDSs, 3,439 proteins could be assigned to Cluster of Orthologous Groups (COG) families (9). One thousand nine hundred fifty-four proteins have orthologs (bit score of Ͼ60) with the five reference strains, Halomonas elongata and four others, Chromohalobacter salexigens DSM 3043, Hahella chejuensis KCTC 2396, Cellvibrio japonicas Ueda107, and Pseudomonas entomophila L48, identified by RAST as the closest neighbors to HAL1.The Halomonas sp. strain HAL1 genome carries multiple genes potentially involved in arsenic resistance. There are two arsenic resistance operons containing genes encoding ArsC, ArsH, and ACR3 but only one operon with a gene encoding ArsR. One of these operons is adjacent to two genes, aioA and aioB, that encode the enzyme arsenite oxidase (4, 7). There is also a pst operon in the immediate vicinity of this arsenic cluster that might play a role in integrating phosphate and arsenic metabolism. In addition, there is another pst operon on the chromosome. Furthermore, a num...

The fixation of dinitrogen (N2) and denitrification are two opposite processes in the nitrogen cycle. The former transfers atmospheric dinitrogen gas into bound nitrogen in the biosphere, while the latter returns this bound nitrogen back to atmospheric dinitrogen. It is unclear whether or not these processes are intimately connected in any microbial ecosystem or that they are spatially and/or temporally separated. Here, we measured seafloor nitrogen fixation and denitrification as well as pelagic nitrogen fixation by using the stable isotope technique. Alongside, we measured the diversity, abundance, and activity of nitrogen-fixing and denitrifying microorganisms at three stations in the southern North Sea. Nitrogen fixation ranged from undetectable to 2.4 nmol N L−1 d−1 and from undetectable to 8.2 nmol N g−1 d−1 in the water column and seafloor, respectively. The highest rates were measured in August at Doggersbank, both for the water column and for the seafloor. Denitrification ranged from 1.7 to 208.8 μmol m−2 d−1 and the highest rates were measured in May at the Oyster Grounds. DNA sequence analysis showed sequences of nifH, a structural gene for nitrogenase, related to sequences from anaerobic sulfur/iron reducers and sulfate reducers. Sequences of the structural gene for nitrite reductase, nirS, were related to environmental clones from marine sediments. Quantitative polymerase chain reaction (qPCR) data revealed the highest abundance of nifH and nirS genes at the Oyster Grounds. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) data revealed the highest nifH expression at Doggersbank and the highest nirS expression at the Oyster Grounds. The distribution of the diazotrophic and denitrifying communities seems to be subject to different selecting factors, leading to spatial and temporal separation of nitrogen fixation and denitrification. These selecting factors include temperature, organic matter availability, and oxygen concentration.

The first step of nitrification, the oxidation of ammonia to nitrite, can be performed by ammonia-oxidizing archaea (AOA) or ammonium-oxidizing bacteria (AOB). We investigated the presence of these two groups in three structurally different types of coastal microbial mats that develop along the tidal gradient on the North Sea beach of the Dutch barrier island Schiermonnikoog. The abundance and transcription of amoA, a gene encoding for the alpha subunit of ammonia monooxygenase that is present in both AOA and AOB, were assessed and the potential nitrification rates in these mats were measured. The potential nitrification rates in the three mat types were highest in autumn and lowest in summer. AOB and AOA amoA genes were present in all three mat types. The composition of the AOA and AOB communities in the mats of the tidal and intertidal stations, based on the diversity of amoA, were similar and clustered separately from the supratidal microbial mat. In all three mats AOB amoA genes were significantly more abundant than AOA amoA genes. The abundance of neither AOB nor AOA amoA genes correlated with the potential nitrification rates, but AOB amoA transcripts were positively correlated with the potential nitrification rate. The composition and abundance of amoA genes seemed to be partly driven by salinity, ammonium, temperature, and the nitrate/nitrite concentration. We conclude that AOB are responsible for the bulk of the ammonium oxidation in these coastal microbial mats.