We analyzed the variation with depth in the composition of members of the domain Bacteria in samples from alkaline, hypersaline, and currently meromictic Mono Lake in California. DNA samples were collected from the mixolimnion (2 m), the base of the oxycline (17.5 m), the upper chemocline (23 m), and the monimolimnion (35 m). Composition was assessed by sequencing randomly selected cloned fragments of 16S rRNA genes retrieved from the DNA samples. Most of the 212 sequences retrieved from the samples fell into five major lineages of the domain Bacteria: ␣-and ␥-Proteobacteria (6 and 10%, respectively), Cytophaga-FlexibacterBacteroides (19%), high-G؉C-content gram-positive organisms (Actinobacteria; 25%), and low-G؉C-content gram-positive organisms (Bacillus and Clostridium; 19%). Twelve percent were identified as chloroplasts. The remaining 9% represented ␤-and ␦-Proteobacteria, Verrucomicrobiales, and candidate divisions. Mixolimnion and oxycline samples had low microbial diversity, with only 9 and 12 distinct phylotypes, respectively, whereas chemocline and monimolimnion samples were more diverse, containing 27 and 25 phylotypes, respectively. The compositions of microbial assemblages from the mixolimnion and oxycline were not significantly different from each other (P ‫؍‬ 0.314 and 0.877), but they were significantly different from those of chemocline and monimolimnion assemblages (P < 0.001), and the compositions of chemocline and monimolimnion assemblages were not significantly different from each other (P ‫؍‬ 0.006 and 0.124). The populations of sequences retrieved from the mixolimnion and oxycline samples were dominated by sequences related to high-G؉C-content grampositive bacteria (49 and 63%, respectively) distributed in only three distinct phylotypes, while the population of sequences retrieved from the monimolimnion sample was dominated (52%) by sequences related to low-G؉C-content gram-positive bacteria distributed in 12 distinct phylotypes. Twelve and 28% of the sequences retrieved from the chemocline sample were also found in the mixolimnion and monimolimnion samples, respectively. None of the sequences retrieved from the monimolimnion sample were found in the mixolimnion or oxycline samples. Elevated diversity in anoxic bottom water samples relative to oxic surface water samples suggests a greater opportunity for niche differentiation in bottom versus surface waters of this lake.Understanding the factors that control the composition and diversity of microbial communities is important to understanding how bacterial populations function to facilitate biogeochemical processes. Mono Lake is an ideal site for such studies because it has strong geochemical gradients, a simple food web, and a relatively simple microbial community. Mono Lake is an alkaline (pH 9.8), hypersaline (84 to 94 g liter Ϫ1 ) soda lake located east of the Sierra Nevada mountains, approximately 160 km south of Lake Tahoe, Calif. Because of the contrast between the density of saline lake water and freshwater flowing into soda lakes, ...

We used massively parallel sequencing (pyrosequencing) of 16S rRNA genes to compare the composition of microbial communities in the guts of 12 bony fish and 3 shark species. The species analyzed encompass herbivores and carnivores with varied digestive physiologies, are classified as pelagic and demersal species, and reside in estuarine to marine environments. We also compared the gut microbial assemblages of wild and cultured Fundulus heteroclitus and of juvenile and adult Lagodon rhomboides. A total of 1 214 355 sequences were filtered, denoised, trimmed, and then sorted into operational taxonomic units (OTUs) based on 97% sequence similarity. Bacteria representing 17 phyla were found among the sampled fish, with most fish hosting between 7 and 15 phyla. Proteobacteria OTUs were present in all fish and often dominated the libraries (3.0 to 98%; average: 61%). Firmicutes were also prevalent, but at a lower relative abundance, ranging between 1.3 and 45% (average: 17%). In most cases, the gut microflora of individual fish of a given species contained many of the same OTUs; however, some species (e.g. great barracuda) shared few OTUs among the individuals sampled. Although no single OTU was shared among all fish species, many of the OTUs present in one species' core group were also found in the core groups of other species. Several OTUs were consistently found in the guts of multiple species, suggesting that these OTUs may be important contributors to fish gut functions such as digestion, nutrient absorption, and immune response.KEY WORDS: Fish gut · Gut microbiome · 16S rRNA · Gut microflora · 454-pyrosequencing · Shark gut · Core gut microbiome Resale or republication not permitted without written consent of the publisher

Nitrification, the oxidation of NH 4 þ to NO 2 À and subsequently to NO 3 À , plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. The first and rate-limiting step in nitrification is catalyzed by the enzyme ammonia monooxygenase (AmoA). We evaluate the relationships between the abundance of ammoniaoxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes; potential nitrification rates and environmental variables to identify factors influencing AOA abundance and nitrifier activity in estuarine sediments. Our results showed that potential nitrification rates increased as abundance of AOA amoA increased. In contrast, there was no relationship between potential nitrification rates and AOB amoA abundance. This suggests that AOA are significant in estuarine nitrogen cycling. Surprisingly, more of the variability in potential nitrification rates was predicted by salinity and pore water sulfide than by dissolved oxygen history.

We analyzed the phylogenetic composition of bacterioplankton assemblages in 11 Arctic Ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16S rRNA genes. The sequencing effort was directed by denaturing gradient gel electrophoresis (DGGE) screening of samples and the clone libraries. Sequences of 88 clones fell into seven major lineages of the domain Bacteria: ␣ (36%)-, ␥ (32%)-, ␦ (14%)-, and (1%)-Proteobacteria; Cytophaga-Flexibacter-Bacteroides spp. (9%); Verrucomicrobium spp. (6%); and green nonsulfur bacteria (2%). A total of 34% of the cloned sequences (excluding clones in the SAR11 and Roseobacter groups) had sequence similarities that were <94% compared to previously reported sequences, indicating the presence of novel sequences. DGGE fingerprints of the selected samples showed that most of the bands were common to all samples in all three seasons. However, additional bands representing sequences related to Cytophaga and Polaribacter species were found in samples collected during the summer and fall. Of the clones in a library generated from one sample collected in spring of 1995, 50% were the same and were most closely affiliated (99% similarity) with Alteromonas macleodii, while 50% of the clones in another sample were most closely affiliated (90 to 96% similarity) with Oceanospirillum sp. The majority of the cloned sequences were most closely related to uncultured, environmental sequences. Prominent among these were members of the SAR11 group. Differences between mixed-layer and halocline samples were apparent in DGGE fingerprints and clone libraries. Sequences related to ␣-Proteobacteria (dominated by SAR11) were abundant (52%) in samples from the mixed layer, while sequences related to ␥-proteobacteria were more abundant (44%) in halocline samples. Two bands corresponding to sequences related to SAR307 (common in deep water) and the high-G؉C gram-positive bacteria were characteristic of the halocline samples.Studies of the biogeography of marine bacteria have become feasible as a result of the application of molecular biological techniques to environmental sciences (13). For example, Fuhrman et al. (20) and Mullins et al. (35) compared the phylogenetic diversity of populations from similar latitudes in the Atlantic and Pacific by using 16S rRNA gene sequences. These studies and studies like them (reviewed in reference 21) have concluded that broad classes of bacterioplankton tend to be cosmopolitan, a conclusion supported by incidental observations made as additional sequences are obtained from samples collected at other locations. However, these studies primarily address distributions in temperate and tropical waters where barriers to genetic exchange have been minimal.Paleo-oceanographic evidence suggests that the Earth's polar oceans are relatively new features of the global marine environment and that, unlike temperate and tropical oceans, they evolved separately. A deepwater connection between the Arctic Ocean ba...

Arsenite [As(III)]-enriched anoxic bottom water from Mono Lake, California, produced arsenate [As(V)] during incubation with either nitrate or nitrite. No such oxidation occurred in killed controls or in live samples incubated without added nitrate or nitrite. A small amount of biological As(III) oxidation was observed in samples amended with Fe(III) chelated with nitrolotriacetic acid, although some chemical oxidation was also evident in killed controls. A pure culture, strain MLHE-1, that was capable of growth with As(III) as its electron donor and nitrate as its electron acceptor was isolated in a defined mineral salts medium. Cells were also able to grow in nitrate-mineral salts medium by using H 2 or sulfide as their electron donor in lieu of As(III). Arsenite-grown cells demonstrated dark 14 CO 2 fixation, and PCR was used to indicate the presence of a gene encoding ribulose-1,5-biphosphate carboxylase/oxygenase. Strain MLHE-1 is a facultative chemoautotroph, able to grow with these inorganic electron donors and nitrate as its electron acceptor, but heterotrophic growth on acetate was also observed under both aerobic and anaerobic (nitrate) conditions. Phylogenetic analysis of its 16S ribosomal DNA sequence placed strain MLHE-1 within the haloalkaliphilic Ectothiorhodospira of the ␥-Proteobacteria. Arsenite oxidation has never been reported for any members of this subgroup of the Proteobacteria.Arsenic (As) is a known carcinogen in drinking water, occurring therein primarily as arsenate [As(V)] or as arsenite [As(III)], with the latter oxyanion having greater toxicity and hydrologic mobility than the former (10). Although various chemical agents can drive the redox reactions occurring between the As(V) and As(III) species (7, 31), it has been shown that specific microbiological detoxification mechanisms can achieve this as well (5, 30). Recent discoveries have revealed that the biochemical reduction or oxidation of these two inorganic As species can also be coupled with energy conservation in some prokaryotes. Thus, respiratory (dissimilatory) reduction of As(V) is found in several phylogenetically diverse anaerobic Bacteria and Crenarchaeota (28), while the aerobic oxidation of As(III) provides energy for the rapid growth of chemoautotrophic bacteria isolated from gold mines (34, 35).Significant lithotrophic oxidative processes need not necessarily be coupled biochemically with oxygen. Such reactions can occur under anoxic conditions, provided that the oxidant has a higher electrochemical potential than the reductant. Examples of this phenomenon are the bacterial oxidation of Fe(II) with nitrate (44) and the oxidation of phosphite by sulfate reducers (36). Here we explore the potential of oxidants such as nitrate and Fe(III) to be coupled with the microbial oxidation of As(III) to As(V).Arsenic-rich Mono Lake, California, was selected as the source of materials for investigation. The high content of dissolved inorganic arsenic (200 M) in this stratified soda lake (pH 9.8; salinity, 70 to 90 g liter Ϫ1 ) i...