Search

The rise of oxygen in the early Earth atmosphere allowed for a vast expansion of life, including the proliferation of animal life, that could utilize this powerful electron acceptor for new metabolisms. This oxygen requirement has left many organisms vulnerable to oxygen-depleted conditions (i.e., anoxia). These anoxic events in Earth’s aquatic environments allow for free iron (ferruginous) or free sulfide (euxinic) conditions to develop. While much research has been done on the past and present of aquatic anoxia, transiently deoxygenated systems that cycle annually between oxygenated and anoxic states are underexplored. Questions about these cycles of aquatic redox state abound; for example, 1) if benthic sulfur-oxidizing bacteria promote free sulfide at the sediment-water interface in transiently deoxygenated systems 2) if these cycles of anoxia can promote a loss of free iron from the benthic marine environment and 3) if sulfate reducing bacteria are quickly established in lacustrine waters after anoxia develops. The first and second questions will be addressed in this dissertation through a suite of investigations in the transiently deoxygenated Santa Barbara Basin. Porewater geochemistry, sulfate reduction rates, and benthic flux measurements were collected between 2019-2023 under varying oxygen concentrations. We found that sulfur-oxidizing bacterial mats in the basin are associated with high rates of dissimilatory nitrate reduction to ammonium and require an elevation of the sulfate reduction zone to the sediment-water interface in order to proliferate. Mat proliferation also requires an exhaustion of iron oxides in the surface sediment. Mat formation is also associated with extremely high fluxes of iron into the water column. This free iron is potentially lost from the basin through bottom water currents that carry mid-waters upslope during the anoxic events.The third question will be addressed in this dissertation by several geochemical and ex-situ sulfate

Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus–host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevance

Prokaryotic diversity in Aran-Bidgol salt lake, a thalasohaline lake in Iran, was studied by fluorescence in situ hybridization (FISH), cultivation techniques, denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of 16S rRNA genes and 16S rRNA gene clone library analysis. Viable counts obtained (2.5–4 × 106 cells mL−1) were similar to total cell abundance in the lake determined by DAPI direct count (3–4×107 cells mL−1). The proportion of Bacteria to Archaea in the community detectable by FISH was unexpectedly high and ranged between 1:3 and 1:2. We analyzed 101 archaeal isolates and found that most belonged to the genera Halorubrum (55%) and Haloarcula (18%). Eleven bacterial isolates obtained in pure culture were affiliated with the genera Salinibacter (18.7%), Salicola (18.7%) and Rhodovibrio (35.3%). Analysis of inserts of 100 clones from the eight 16S rRNA clone libraries constructed revealed 37 OTUs. The majority (63%) of these sequences were not related to any previously identified taxa. Within this sampling effort we most frequently retrieved phylotypes related to Halorhabdus (16% of archaeal sequences obtained) and Salinibacter (36% of bacterial sequences obtained). Other prokaryotic groups that were abundant included representatives of Haloquadratum, the anaerobic genera Halanaerobium and Halocella, purple sulfur bacteria of the genus Halorhodospira and Cyanobacteria.

Prokaryotic diversity in Aran-Bidgol salt lake, a thalasohaline lake in Iran, was studied by fluorescence in situ hybridization (FISH), cultivation techniques, denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of 16S rRNA genes and 16S rRNA gene clone library analysis. Viable counts obtained (2.5–4 × 106 cells mL−1) were similar to total cell abundance in the lake determined by DAPI direct count (3–4×107 cells mL−1). The proportion of Bacteria to Archaea in the community detectable by FISH was unexpectedly high and ranged between 1:3 and 1:2. We analyzed 101 archaeal isolates and found that most belonged to the genera Halorubrum (55%) and Haloarcula (18%). Eleven bacterial isolates obtained in pure culture were affiliated with the genera Salinibacter (18.7%), Salicola (18.7%) and Rhodovibrio (35.3%). Analysis of inserts of 100 clones from the eight 16S rRNA clone libraries constructed revealed 37 OTUs. The majority (63%) of these sequences were not related to any previously identified taxa. Within this sampling effort we most frequently retrieved phylotypes related to Halorhabdus (16% of archaeal sequences obtained) and Salinibacter (36% of bacterial sequences obtained). Other prokaryotic groups that were abundant included representatives of Haloquadratum, the anaerobic genera Halanaerobium and Halocella, purple sulfur bacteria of the genus Halorhodospira and Cyanobacteria.

Two proteolytic bacterial strains, BSker2Tand BSker3T, were enriched from sediments of hypersaline alkaline lakes in Kulunda Steppe (Altai, Russia) with chicken feathers as substrate, followed by pure culture isolation on hypersaline alkaline media with casein. The cells were non-motile, filamentous, flexible rods. The isolates were obligately aerobic heterotrophs utilizing proteins and peptides as growth substrates. Both were obligate alkaliphiles, but differed in their pH optimum for growth: pH 9.5-9.8 for Bsker2Tand pH 8.5-8.8 for BSker3T. The salt range for growth of both isolates was between 2 and 4.5 M total Na+ with an optimum at 2.5-3 M. No organic osmolytes were detected in cells of BSker2T, but they accumulated high intracellular concentrations of K+. The polar lipid fatty acids were dominated by unsaturated C16 and C18 species. The 16S rRNA gene phylogeny indicated that both strains belong to the recently proposed phylum Rhodothermaeota. BSker2Tforms a novel genus-level branch, while BSker3Trepresents a novel species-level member in the genus Longimonas. On the basis of distinct phenotypic and genotypic properties, strain BSker2T(=JCM 31342T=UNIQEM U1009T) is proposed to be classified as a representative of a novel genus and species, Natronotalea proteinilyticagen. nov., sp. nov., and strain BSker3T(=JCM 31343T=UNIQEM U1010T) as a representative of a novel species, Longimonas haloalkaliphila sp. nov., Accepted Author Manuscript, BT/Environmental Biotechnology

Prokaryotic diversity in Aran-Bidgol salt lake, a thalasohaline lake in Iran, was studied by fluorescence in situ hybridization (FISH), cultivation techniques, denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of 16S rRNA genes and 16S rRNA gene clone library analysis. Viable counts obtained (2.5–4 × 106 cells mL−1) were similar to total cell abundance in the lake determined by DAPI direct count (3–4×107 cells mL−1). The proportion of Bacteria to Archaea in the community detectable by FISH was unexpectedly high and ranged between 1:3 and 1:2. We analyzed 101 archaeal isolates and found that most belonged to the genera Halorubrum (55%) and Haloarcula (18%). Eleven bacterial isolates obtained in pure culture were affiliated with the genera Salinibacter (18.7%), Salicola (18.7%) and Rhodovibrio (35.3%). Analysis of inserts of 100 clones from the eight 16S rRNA clone libraries constructed revealed 37 OTUs. The majority (63%) of these sequences were not related to any previously identified taxa. Within this sampling effort we most frequently retrieved phylotypes related to Halorhabdus (16% of archaeal sequences obtained) and Salinibacter (36% of bacterial sequences obtained). Other prokaryotic groups that were abundant included representatives of Haloquadratum, the anaerobic genera Halanaerobium and Halocella, purple sulfur bacteria of the genus Halorhodospira and Cyanobacteria.

Prokaryotic diversity in Aran-Bidgol salt lake, a thalasohaline lake in Iran, was studied by fluorescence in situ hybridization (FISH), cultivation techniques, denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of 16S rRNA genes and 16S rRNA gene clone library analysis. Viable counts obtained (2.5–4 × 106 cells mL−1) were similar to total cell abundance in the lake determined by DAPI direct count (3–4×107 cells mL−1). The proportion of Bacteria to Archaea in the community detectable by FISH was unexpectedly high and ranged between 1:3 and 1:2. We analyzed 101 archaeal isolates and found that most belonged to the genera Halorubrum (55%) and Haloarcula (18%). Eleven bacterial isolates obtained in pure culture were affiliated with the genera Salinibacter (18.7%), Salicola (18.7%) and Rhodovibrio (35.3%). Analysis of inserts of 100 clones from the eight 16S rRNA clone libraries constructed revealed 37 OTUs. The majority (63%) of these sequences were not related to any previously identified taxa. Within this sampling effort we most frequently retrieved phylotypes related to Halorhabdus (16% of archaeal sequences obtained) and Salinibacter (36% of bacterial sequences obtained). Other prokaryotic groups that were abundant included representatives of Haloquadratum, the anaerobic genera Halanaerobium and Halocella, purple sulfur bacteria of the genus Halorhodospira and Cyanobacteria.

Prokaryotic diversity in Aran-Bidgol salt lake, a thalasohaline lake in Iran, was studied by fluorescence in situ hybridization (FISH), cultivation techniques, denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of 16S rRNA genes and 16S rRNA gene clone library analysis. Viable counts obtained (2.5–4 × 106 cells mL−1) were similar to total cell abundance in the lake determined by DAPI direct count (3–4×107 cells mL−1). The proportion of Bacteria to Archaea in the community detectable by FISH was unexpectedly high and ranged between 1:3 and 1:2. We analyzed 101 archaeal isolates and found that most belonged to the genera Halorubrum (55%) and Haloarcula (18%). Eleven bacterial isolates obtained in pure culture were affiliated with the genera Salinibacter (18.7%), Salicola (18.7%) and Rhodovibrio (35.3%). Analysis of inserts of 100 clones from the eight 16S rRNA clone libraries constructed revealed 37 OTUs. The majority (63%) of these sequences were not related to any previously identified taxa. Within this sampling effort we most frequently retrieved phylotypes related to Halorhabdus (16% of archaeal sequences obtained) and Salinibacter (36% of bacterial sequences obtained). Other prokaryotic groups that were abundant included representatives of Haloquadratum, the anaerobic genera Halanaerobium and Halocella, purple sulfur bacteria of the genus Halorhodospira and Cyanobacteria.

Two proteolytic bacterial strains, BSker2Tand BSker3T, were enriched from sediments of hypersaline alkaline lakes in Kulunda Steppe (Altai, Russia) with chicken feathers as substrate, followed by pure culture isolation on hypersaline alkaline media with casein. The cells were non-motile, filamentous, flexible rods. The isolates were obligately aerobic heterotrophs utilizing proteins and peptides as growth substrates. Both were obligate alkaliphiles, but differed in their pH optimum for growth: pH 9.5-9.8 for Bsker2Tand pH 8.5-8.8 for BSker3T. The salt range for growth of both isolates was between 2 and 4.5 M total Na+ with an optimum at 2.5-3 M. No organic osmolytes were detected in cells of BSker2T, but they accumulated high intracellular concentrations of K+. The polar lipid fatty acids were dominated by unsaturated C16 and C18 species. The 16S rRNA gene phylogeny indicated that both strains belong to the recently proposed phylum Rhodothermaeota. BSker2Tforms a novel genus-level branch, while BSker3Trepresents a novel species-level member in the genus Longimonas. On the basis of distinct phenotypic and genotypic properties, strain BSker2T(=JCM 31342T=UNIQEM U1009T) is proposed to be classified as a representative of a novel genus and species, Natronotalea proteinilyticagen. nov., sp. nov., and strain BSker3T(=JCM 31343T=UNIQEM U1010T) as a representative of a novel species, Longimonas haloalkaliphila sp. nov., Accepted Author Manuscript, BT/Environmental Biotechnology

Despite compiling evidence on distribution of organohalide-respiring bacteria (OHRB) in pristine environments, there is lack of knowledge about their occurrence and potential contribution to the chlorine cycle in extreme environments such as hypersaline lakes. Biotic formation of organohalides (OHs) such as chloromethane and chloroform was recently reported from the hypersaline Lake Strawbridge, Australia. Assuming that natural availability of OHs can prime development of organohalide respiration potential, we prepared microcosms from Lake Strawbridge sediments. Amended chloroform and tetrachloroethene (PCE) were stoichiometrically dechlorinated to dichloromethane and trichloroethene, respectively. MiSeq 16S ribosomal RNA gene analysis and quantitative PCR did not detect any known chloroform and PCE-dechlorinating OHRB in anaerobic sediment microcosms and transfers, which indicated the presence of novel OHRB in hypersaline Lake Strawbridge. To our knowledge, this is the first report on OHR occurrence in extreme pristine environments. Combined with the formerly documented biotic chlorination, this suggests interdependencies between microbial chlorinators and dechlorinators in the local chlorine cycle in an extreme ecosystem.

Strain M27-SA2 was isolated from the deep-sea salt-saturated anoxic lake Medee, which represents one of the most hostile extreme environments on our planet. On the basis of physiological studies and phylogenetic positioning this extremely halophilic euryarchaeon belongs to a novel genus 'Halanaeroarchaeum' within the family Halobacteriaceae. All members of this genus cultivated so far are strict anaerobes using acetate as the sole carbon and energy source and elemental sulfur as electron acceptor. Here we report the complete genome sequence of the strain M27-SA2 which is composed of a 2,129,244-bp chromosome and a 124,256-bp plasmid. This is the second complete genome sequence within the genus Halanaeroarchaeum. We demonstrate that genome of 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors complete metabolic pathways for acetate and sulfur catabolism and for de novo biosynthesis of 19 amino acids. The genomic analysis also reveals that 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors two prophage loci and one CRISPR locus, highly similar to that of Kulunda Steppe (Altai, Russia) isolate 'H. sulfurireducens' HSR2T. The discovery of sulfur-respiring acetate-utilizing haloarchaeon in deep-sea hypersaline anoxic lakes has certain significance for understanding the biogeochemical functioning of these harsh ecosystems, which are incompatible with life for common organisms. Moreover, isolations of Halanaeroarchaeum members from geographically distant salt-saturated sites of different origin suggest a high degree of evolutionary success in their adaptation to this type of extreme biotopes around the world., BT/Environmental Biotechnology

Strain M27-SA2 was isolated from the deep-sea salt-saturated anoxic lake Medee, which represents one of the most hostile extreme environments on our planet. On the basis of physiological studies and phylogenetic positioning this extremely halophilic euryarchaeon belongs to a novel genus 'Halanaeroarchaeum' within the family Halobacteriaceae. All members of this genus cultivated so far are strict anaerobes using acetate as the sole carbon and energy source and elemental sulfur as electron acceptor. Here we report the complete genome sequence of the strain M27-SA2 which is composed of a 2,129,244-bp chromosome and a 124,256-bp plasmid. This is the second complete genome sequence within the genus Halanaeroarchaeum. We demonstrate that genome of 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors complete metabolic pathways for acetate and sulfur catabolism and for de novo biosynthesis of 19 amino acids. The genomic analysis also reveals that 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors two prophage loci and one CRISPR locus, highly similar to that of Kulunda Steppe (Altai, Russia) isolate 'H. sulfurireducens' HSR2T. The discovery of sulfur-respiring acetate-utilizing haloarchaeon in deep-sea hypersaline anoxic lakes has certain significance for understanding the biogeochemical functioning of these harsh ecosystems, which are incompatible with life for common organisms. Moreover, isolations of Halanaeroarchaeum members from geographically distant salt-saturated sites of different origin suggest a high degree of evolutionary success in their adaptation to this type of extreme biotopes around the world., BT/Environmental Biotechnology

Urmia Lake is the largest habitat of Artemia Urmiana in the world located in an endorheic basin in northwest Iran. This shallow terminal lake has been designated as a Biosphere Reserve by UNESCO and a National Park under the 1971 Ramsar Convention. Currently, the entire lake’s watershed is threatened due to its abrupt desiccation of more than 50% of its surface area and the concomitant increase of salinity during the last two decades. As the rapidly declining eco-environmental conditions have serious impacts on the socio-economy of the whole region, the drying of the lake is considered as a national threat. In light of the above, within the present study a holistic hydroclimatic analysis of the lake is conducted. The principal hypothesis of this research is that ‘during the recent years (1996-2012), there has been an intrinsic change in the dynamic of the lake water level mainly due to human activities which has had deteriorating impacts on the lake and its entire basin’. Therefore, water level variations, as the eco-hydrological indicator of this basin, are compared for the two periods of natural and anthropogenically intervened i.e. 1966-1995 and 1996-2012, respectively. The result of Mann-Kendall trend test, which has been used to identify the changes, shows that there is a unique decreasing trend of about -0.25 m/yr in average during the recent period of 1996-2012. Further, the nonlinear chaotic analysis of Correlation Dimension Method is employed in order to investigate the underlying dynamic of water level oscillations. The correlation exponent has decreased from 3 during the period of 1966-1995 to 2 during 1966-2012 implying that 1 governing variable of the lake’s dynamic is missing! Pursuing the major cause of the recent desiccations, a multiple linear regression model is made based on the standardized monthly anomalies of the lake water level during 1966-1995 and the influencing teleconnection indices as predictors. For the months March and April as high se

Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.