Alcalilimnicola halodurans gen. nov., sp. nov., an alkaliphilic, moderately halophilic and extremely halotolerant bacterium, isolated from sediments of soda-depositing Lake Natron, East Africa Rift Valley.

bRecent metagenomic studies on saltern ponds with intermediate salinities have determined that their microbial communities are dominated by both Euryarchaeota and halophilic bacteria, with a gammaproteobacterium closely related to the genera Alkalilimnicola and Arhodomonas being one of the most predominant microorganisms, making up to 15% of the total prokaryotic population. Here we used several strategies and culture media in order to isolate this organism in pure culture. We report the isolation and taxonomic characterization of this new, never before cultured microorganism, designated M19-40 T , isolated from a saltern located in Isla Cristina, Spain, using a medium with a mixture of 15% salts, yeast extract, and pyruvic acid as the carbon source. Morphologically small curved cells (young cultures) with a tendency to form long spiral cells in older cultures were observed in pure cultures. The organism is a Gram-negative, nonmotile bacterium that is strictly aerobic, non-endospore forming, heterotrophic, and moderately halophilic, and it is able to grow at 10 to 25% (wt/vol) NaCl, with optimal growth occurring at 15% (wt/ vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that strain M19-40 T has a low similarity with other previously described bacteria and shows the closest phylogenetic similarity with species of the genera Alkalilimnicola (94.9 to 94.5%), Alkalispirillum (94.3%), and Arhodomonas (93.9%) within the family Ectothiorhodospiraceae. The phenotypic, genotypic, and chemotaxonomic features of this new bacterium showed that it constitutes a new genus and species, for which the name Spiribacter salinus gen. nov., sp. nov., is proposed, with strain M19-40 T ‫؍(‬ CECT 8282 T ‫؍‬ IBRC-M 10768 T ‫؍‬ LMG 27464 T ) being the type strain.

Section: Resultssupporting

confidence: 67%

From Metagenomics to Pure Culture: Isolation and Characterization of the Moderately Halophilic Bacterium Spiribacter salinus gen. nov., sp. nov

León

Fernández

Ghai

et al. 2014

“…PCRs were treated with SeqMix (QBiogene, Irvine, CA) prior to sequencing reactions according to the manufacturer's instructions. The SSU rRNA gene was amplified with the universal primers FD1 (5Ј-AGAGTTTGATCCTGGCTCAG-3Ј) and 1540R (5Ј-GGAGGTG WTCCARCCGC-3Ј) as previously described (54).…”

Section: Methodsmentioning

confidence: 99%

Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China

Jiang

Dong

Zhang

et al. 2006

382

217

We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 10 8 cells/g at the water-sediment interface to 10 7 cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with the Bacteroidetes were the most abundant, whereas in the sediments, sequences related to low G؉C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to the Halobacteriales, the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.

“…It was also 92% similar to a bacterium (MLHE-1) (49) isolated from Mono Lake. A. halodurans is an alkaliphilic, extremely halotolerant bacterium isolated from the sediment of soda-depositing Lake Natron, Tanzania (72). A. mobile is a moderately halophilic, alkaliphilic, gram-negative, obligate aerobe (58).…”

Section: Resultsmentioning

confidence: 99%

Depth Distribution of Microbial Diversity in Mono Lake, a Meromictic Soda Lake in California

Humayoun

Bano

Hollibaugh

2003

324

266

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, ...