Effects of Imposed Salinity Gradients on Dissimilatory Arsenate Reduction, Sulfate Reduction, and Other Microbial Processes in Sediments from Two California Soda Lakes

ABSTRACT Salinity effects on microbial community structure and on potential rates of arsenate reduction, arsenite oxidation, sulfate reduction, denitrification, and methanogenesis were examined in sediment slurries from two California soda lakes. We conducted experiments with Mono Lake and Searles Lake sediments over a wide range of salt concentrations (25 to 346 g liter−1). With the exception of sulfate reduction, rates of all processes demonstrated an inverse relationship to total salinity. However, each of these processes persisted at low but detectable rates at salt saturation. Denaturing gradient gel electrophoresis analysis of partial 16S rRNA genes amplified from As(V) reduction slurries revealed that distinct microbial populations grew at low (25 to 50 g liter−1), intermediate (100 to 200 g liter−1), and high (>300 g liter−1) salinity. At intermediate and high salinities, a close relative of a cultivated As-respiring halophile was present. These results suggest that organisms adapted to more dilute conditions can remain viable at high salinity and rapidly repopulate the lake during periods of rising lake level. In contrast to As reduction, sulfate reduction in Mono Lake slurries was undetectable at salt saturation. Furthermore, sulfate reduction was excluded from Searles Lake sediments at any salinity despite the presence of abundant sulfate. Sulfate reduction occurred in Searles Lake sediment slurries only following inoculation with Mono Lake sediment, indicating the absence of sulfate-reducing flora. Experiments with borate-amended Mono Lake slurries suggest that the notably high (0.46 molal) concentration of borate in the Searles Lake brine was responsible for the exclusion of sulfate reducers from that ecosystem.

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Dissimilatory Arsenate and Sulfate Reduction in Sediments of Two Hypersaline, Arsenic-Rich Soda Lakes: Mono and Searles Lakes, California

Applied and Environmental Microbiology ◽

10.1128/aem.01066-06 ◽

2006 ◽

Vol 72 (10) ◽

pp. 6514-6526 ◽

Cited By ~ 91

Author(s):

T. R. Kulp ◽

S. E. Hoeft ◽

L. G. Miller ◽

C. Saltikov ◽

J. N. Murphy ◽

...

Keyword(s):

Sulfate Reduction ◽

Denaturing Gradient Gel Electrophoresis ◽

Soda Lakes ◽

Mono Lake ◽

16S Rrna Genes ◽

Rrna Genes ◽

Radioisotope Method ◽

Reduction Activity ◽

Gradient Gel Electrophoresis ◽

Arsenate Reduction

ABSTRACT A radioisotope method was devised to study bacterial respiratory reduction of arsenate in sediments. The following two arsenic-rich soda lakes in California were chosen for comparison on the basis of their different salinities: Mono Lake (∼90 g/liter) and Searles Lake (∼340 g/liter). Profiles of arsenate reduction and sulfate reduction were constructed for both lakes. Reduction of [73As]arsenate occurred at all depth intervals in the cores from Mono Lake (rate constant [k] = 0.103 to 0.04 h−1) and Searles Lake (k = 0.012 to 0.002 h−1), and the highest activities occurred in the top sections of each core. In contrast, [35S]sulfate reduction was measurable in Mono Lake (k = 7.6 ×104 to 3.2 × 10−6 h−1) but not in Searles Lake. Sediment DNA was extracted, PCR amplified, and separated by denaturing gradient gel electrophoresis (DGGE) to obtain phylogenetic markers (i.e., 16S rRNA genes) and a partial functional gene for dissimilatory arsenate reduction (arrA). The amplified arrA gene product showed a similar trend in both lakes; the signal was strongest in surface sediments and decreased to undetectable levels deeper in the sediments. More arrA gene signal was observed in Mono Lake and was detectable at a greater depth, despite the higher arsenate reduction activity observed in Searles Lake. A partial sequence (about 900 bp) was obtained for a clone (SLAS-3) that matched the dominant DGGE band found in deeper parts of the Searles Lake sample (below 3 cm), and this clone was found to be closely related to SLAS-1, a novel extremophilic arsenate respirer previously cultivated from Searles Lake.

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Fractionation of stable carbon isotopes during acetate consumption by methanogenic and sulfidogenic microbial communities in rice paddy soils and lake sediments

10.5194/bg-2021-203 ◽

2021 ◽

Author(s):

Ralf Conrad ◽

Pengfei Liu ◽

Peter Claus

Keyword(s):

Microbial Communities ◽

Lake Sediments ◽

Lake Sediment ◽

Enrichment Factors ◽

The Philippines ◽

Paddy Soils ◽

16S Rrna Genes ◽

Rrna Genes ◽

North East ◽

Aceticlastic Methanogenesis

Abstract. Acetate is an important intermediate during the degradation of organic matter in anoxic flooded soils and sediments. Acetate is disproportionated to CH4 and CO2 by methanogenic or is oxidized to CO2 by sulfate-reducing microorganisms. These reactions result in carbon isotope fractionation, depending on the microbial species and their particular carbon metabolism. To learn more about the magnitude of the isotopic enrichment factors (ε) involved, acetate conversion to CH4 and CO2 was measured in anoxic paddy soils from Vercelli (Italy) and the International Rice Research Institute (IRRI, the Philippines) and in anoxic lake sediments from the north east (NE) and the south west (SW) basins of Fuchskuhle (Germany). Acetate consumption was measured using samples of paddy soil or lake sediment suspended in water or in phosphate buffer (pH 7.0), both in the absence and presence of sulfate (gypsum), and of methyl fluoride (CH3F), an inhibitor of aceticlastic methanogenesis. Under methanogenic conditions, values of εac for acetate consumption were always in a range of -21 ‰ to -17 ‰, but higher in the lake sediment from the SW basin (-11 ‰). Under sulfidogenic conditions εac values tended to be slightly lower (-26 ‰ to -19 ‰) especially when aceticlastic methanogenesis was inhibited. Again, εac in the lake sediment of the SW basin was higher (-18 ‰ to -14 ‰). Determination of εCH4 from the accumulation of 13C in CH4 resulted in much lower values (-37 ‰ to -27 ‰) than from the depletion of 13C in acetate (-21 ‰ to -17 ‰), especially when acetate degradation was measured in buffer suspensions. The microbial communities were characterized by sequencing the bacterial 16S rRNA genes as well as the methanogenic mcrA and sulfidogenic dsrB genes. The microbial communities were quite different between lake sediments and paddy soils, but were similar in the sediments of the two lake basins and in the soils from Vercelli and IRR, and were similar after preincubation without and with addition of sulfate (gypsum). The different microbial compositions could hardly serve for the prediction of the magnitude of enrichment factors.

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Chitinase Genes in Lake Sediments of Ardley Island, Antarctica

Applied and Environmental Microbiology ◽

10.1128/aem.71.12.7904-7909.2005 ◽

2005 ◽

Vol 71 (12) ◽

pp. 7904-7909 ◽

Cited By ~ 58

Author(s):

Xiang Xiao ◽

Xuebin Yin ◽

Jian Lin ◽

Liguang Sun ◽

Ziyong You ◽

...

Keyword(s):

Bacterial Community ◽

Lake Sediment ◽

Sediment Core ◽

Chitinase Gene ◽

16S Rrna Genes ◽

Rrna Genes ◽

Chitinolytic Bacteria ◽

Organic Carbon Concentration ◽

Gene Copies ◽

Chitinase Genes

ABSTRACT A sediment core spanning approximately 1,600 years was collected from a lake on Ardley Island, Antarctica. The sediment core had been greatly influenced by penguin guano. Using molecular methods, the chitinolytic bacterial community along the sediment core was studied over its entire length. Primers targeting conserved sequences of the catalytic domains of family 18 subgroup A chitinases detected group A chitinases from a wide taxonomic range of bacteria. Using quantitative competitive PCR (QC-PCR), chitinase gene copies in each 1-cm section of the whole sediment column were quantified. QC-PCR determination of the chitinase gene copies indicated significant correlation with phosphorus and total organic carbon concentration, suggesting a historical connection between chitinase gene copies and the amount of penguin guano input into the lake sediment. Most of the chitinase genes cloned from the historic sediment core were novel. Analysis of the chitinase gene diversity in selected sediment layers and in the fresh penguin deposits indicated frequent shifts in the chitinolytic bacterial community over time. Sequence analysis of the 16S rRNA genes of chitinolytic bacteria isolated from the lake sediment revealed that the isolates belonged to Janthinobacterium species, Stenotrophomonas species of γ-Proteobacteria, Cytophaga species of the Cytophaga-Flexibacter-Bacteroides group, and Streptomyces and Norcardiopsis species of Actinobacteria. Chitinase gene fragments were cloned and sequenced from these cultivated chitinolytic bacteria. The phylogeny of the chitinase genes obtained from the isolates did not correspond well to that of the isolates, suggesting acquisition via horizontal gene transfer.

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

Applied and Environmental Microbiology ◽

10.1128/aem.69.2.1030-1042.2003 ◽

2003 ◽

Vol 69 (2) ◽

pp. 1030-1042 ◽

Cited By ~ 257

Author(s):

Shaheen B. Humayoun ◽

Nasreen Bano ◽

James T. Hollibaugh

Keyword(s):

Microbial Diversity ◽

Water Samples ◽

Soda Lake ◽

Niche Differentiation ◽

Mono Lake ◽

16S Rrna Genes ◽

Rrna Genes ◽

Gram Positive ◽

Gram Positive Bacteria ◽

Surface Water Samples

ABSTRACT 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: α- and γ-Proteobacteria (6 and 10%, respectively), Cytophaga-Flexibacter-Bacteroides (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 β- and δ-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 gram-positive 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.

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Survey of bacteria associated with western corn rootworm life stages reveals no difference between insects reared in different soils

10.1101/365296 ◽

2018 ◽

Author(s):

Dalton C. Ludwick ◽

Aaron C. Ericsson ◽

Lisa N. Meihls ◽

Michelle L.J. Gregory ◽

Deborah L. Finke ◽

...

Keyword(s):

Pest Management ◽

Life Stage ◽

Diabrotica Virgifera Virgifera ◽

Western Corn Rootworm ◽

16S Rrna Genes ◽

Rrna Genes ◽

Corn Rootworm ◽

Life Stages ◽

Wide Range ◽

Different Soils

AbstractWestern corn rootworm (Diabrotica virgifera virgifera LeConte) is a serious pest of maize (Zea mays L.) in North America and parts of Europe. With most of its life cycle spent in the soil feeding on maize root tissues, this insect is likely to encounter and interact with a wide range of soil and rhizosphere microbes. Our knowledge of the role of microbes in pest management and plant health remains incomplete. An important component of an effective pest management strategy is to know which microorganisms are present that could play a role in life history or management. For this study, insects were reared in soils from different locations. Insects were sampled at each life stage to determine the possible core bacteriome. Additionally, soil was sampled at each life stage and resulting bacteria were identified to determine the contribution of soil to the rootworm bacteriome, if any. We analyzed the V4 hypervariable region of bacterial 16S rRNA genes with Illumina MiSeq to survey the different species of bacteria associated with the insects and the soils. The bacterial community associated with insects was significantly different from that in the soil. Some differences appear to exist between insects from non-diapausing and diapausing colonies while no significant differences in community composition existed between the insects reared on different soils. Despite differences in the bacteria present in immature stages and in male and female adults, there is a possible core bacteriome of approximately 16 operational taxonomic units (i.e., present across all life stages). This research may give insights into how resistance to Bt develops, improved nutrition in artificial rearing systems, and new management strategies.

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Cold-Active Shewanella glacialimarina TZS-4T nov. Features a Temperature-Dependent Fatty Acid Profile and Putative Sialic Acid Metabolism

Frontiers in Microbiology ◽

10.3389/fmicb.2021.737641 ◽

2021 ◽

Vol 12 ◽

Author(s):

Muhammad Suleman Qasim ◽

Mirka Lampi ◽

Minna-Maria K. Heinonen ◽

Berta Garrido-Zabala ◽

Dennis H. Bamford ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Sialic Acid ◽

Sea Ice ◽

Acid Metabolism ◽

Elevated Temperatures ◽

Consensus Sequence ◽

16S Rrna Genes ◽

Rrna Genes ◽

Wide Range ◽

Cold Active

Species of genus Shewanella are among the most frequently identified psychrotrophic bacteria. Here, we have studied the cellular properties, growth dynamics, and stress conditions of cold-active Shewanella strain #4, which was previously isolated from Baltic Sea ice. The cells are rod-shaped of ~2μm in length and 0.5μm in diameter, and they grow between 0 and 25°C, with an optimum at 15°C. The bacterium grows at a wide range of conditions, including 0.5–5.5% w/v NaCl (optimum 0.5–2% w/v NaCl), pH 5.5–10 (optimum pH 7.0), and up to 1mM hydrogen peroxide. In keeping with its adaptation to cold habitats, some polyunsaturated fatty acids, such as stearidonic acid (18:4n-3), eicosatetraenoic acid (20:4n-3), and eicosapentaenoic acid (20:5n-3), are produced at a higher level at low temperature. The genome is 4,456kb in size and has a GC content of 41.12%. Uniquely, strain #4 possesses genes for sialic acid metabolism and utilizes N-acetyl neuraminic acid as a carbon source. Interestingly, it also encodes for cytochrome c3 genes, which are known to facilitate environmental adaptation, including elevated temperatures and exposure to UV radiation. Phylogenetic analysis based on a consensus sequence of the seven 16S rRNA genes indicated that strain #4 belongs to genus Shewanella, closely associated with Shewanella aestuarii with a ~97% similarity, but with a low DNA–DNA hybridization (DDH) level of ~21%. However, average nucleotide identity (ANI) analysis defines strain #4 as a separate Shewanella species (ANI score=76). Further phylogenetic analysis based on the 92 most conserved genes places Shewanella strain #4 into a distinct phylogenetic clade with other cold-active marine Shewanella species. Considering the phylogenetic, phenotypic, and molecular characterization, we conclude that Shewanella strain #4 is a novel species and name it Shewanella glacialimarina sp. nov. TZS-4T, where glacialimarina means sea ice. Consequently, S. glacialimarina TZS-4T constitutes a promising model for studying transcriptional and translational regulation of cold-active metabolism.

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In-depth analysis of Bacillus anthracis 16S rRNA genes and transcripts reveals intra- and intergenomic diversity and facilitates anthrax detection

10.1101/2021.08.02.454851 ◽

2021 ◽

Author(s):

Peter Braun ◽

Fee Zimmermann ◽

Mathias C Walter ◽

Sonja Mantel ◽

Karin Aistleitner ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Species ◽

16S Rrna Genes ◽

Rrna Genes ◽

Close Relative ◽

Rrna Gene ◽

Copy Numbers ◽

Depth Analysis

Analysis of 16S ribosomal RNA (rRNA) genes provides a central means of taxonomic classification of bacterial species. Based on presumed sequence identity among species of the Bacillus cereus sensu lato group, the 16S rRNA genes of B. anthracis have been considered unsuitable for diagnosis of the anthrax pathogen. With the recent identification of a single nucleotide polymorphism in some 16S rRNA gene copies, specific identification of B. anthracis becomes feasible. Here, we designed and evaluated a set of in situ-, in vitro- and in silico-assays to assess the yet unknown 16S-state of B. anthracis from different perspectives. Using a combination of digital PCR, fluorescence in situ hybridization, long-read genome sequencing and bioinformatics we were able to detect and quantify a unique 16S rRNA gene allele of B. anthracis (16S-BA-allele). This allele was found in all available B. anthracis genomes and may facilitate differentiation of the pathogen from any close relative. Bioinformatics analysis of 959 B. anthracis genome data-sets inferred that abundances and genomic arrangements of the 16S-BA-allele and the entire rRNA operon copy-numbers differ considerably between strains. Expression ratios of 16S-BA-alleles were proportional to the respective genomic allele copy-numbers. The findings and experimental tools presented here provide detailed insights into the intra- and intergenomic diversity of 16S rRNA genes and may pave the way for improved identification of B. anthracis and other pathogens with diverse rRNA operons.

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A Comparative Study: Taxonomic Grouping of Alkaline Protease Producing Bacilli

Polish Journal of Microbiology ◽

10.5604/17331331.1234992 ◽

2017 ◽

Vol 66 (1) ◽

pp. 39-56

Author(s):

Nilgun Tekin ◽

Arzu Coleri Cihan ◽

Basar Karaca ◽

Cumhur Cokmus

Keyword(s):

16S Rrna ◽

Alkaline Protease ◽

Phylogenetic Analyses ◽

Molecular Techniques ◽

16S Rrna Genes ◽

Rrna Genes ◽

Protease Production ◽

Rrna Gene ◽

Wide Range ◽

Its Pcr

Alkaline proteases have biotechnological importance due to their activity and stability at alkaline pH. 56 bacteria, capable of growing under alkaline conditions were isolated and their alkaline protease activities were carried out at different parameters to determine their optimum alkaline protease production conditions. Seven isolates were showed higher alkaline protease production capacity than the reference strains. The highest alkaline protease producing isolates (103125 U/g), E114 and C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates and the results were in concurrence with phylogenetic analyses of the 16S rRNA genes. While ITS-PCR provided the highest correlation with 16S rRNA groups, (GTG)5-PCR showed the highest differentiation at species and intra-species level. In this study, each of the biotechnologically valuable alkaline protease producing isolates was grouped into their taxonomic positions with multi-genotypic analyses.

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Phylogenomic analysis of Anabaenopsis elenkinii (Nostocales, Cyanobacteria)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004648 ◽

2021 ◽

Author(s):

Endrews Delbaje ◽

Ana Paula D. Andreote ◽

Thierry A. Pellegrinetti ◽

Renata B. Cruz ◽

Luis H. Z. Branco ◽

...

Keyword(s):

16S Rrna ◽

Type Species ◽

Soda Lakes ◽

16S Rrna Genes ◽

Rrna Genes ◽

Phylogenomic Analysis ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

The Family

The saline-alkaline lakes (soda lakes) are the habitat of the haloalkaliphilic cyanobacterium Anabaenopsis elenkinii, the type species of this genus. To obtain robust phylogeny of this type species, we have generated whole-genome sequencing of the bloom-forming Anabaenopsis elenkinii strain CCIBt3563 isolated from a Brazilian soda lake. This strain presents the typical morphology of A. elenkinii with short and curved trichomes with apical heterocytes established after separation of paired intercalary heterocytes and also regarding to cell dimensions. Its genome size is 4 495 068 bp, with a G+C content of 41.98 %, a total of 3932 potential protein coding genes and four 16S rRNA genes. Phylogenomic tree inferred by RAxML based on the alignment of 120 conserved proteins using GTDB-Tk grouped A. elenkinii CCIBt3563 together with other genera of the family Aphanizomenonaceae. However, the only previous available genome of Anabaenopsis circularis NIES-21 was distantly positioned within a clade of Desikacharya strains, a genus from the family Nostocaceae. Furthermore, average nucleotide identity values from 86–98 % were obtained among NIES-21 and Desikacharya genomes, while this value was 76.04 % between NIES-21 and the CCIBt3563 genome. These findings were also corroborated by the phylogenetic tree of 16S rRNA gene sequences, which also showed a strongly supported subcluster of A. elenkinii strains from Brazilian, Mexican and Kenyan soda lakes. This study presents the phylogenomics and genome-scale analyses of an Anabaenopsis elenkinii strain, improving molecular basis for demarcation of this species and framework for the classification of cyanobacteria based on the polyphasic approach.

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Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.65000-0 ◽

2007 ◽

Vol 57 (8) ◽

pp. 1855-1867 ◽

Cited By ~ 233

Author(s):

Wei Wei ◽

Robert E. Davis ◽

Ing-Ming Lee ◽

Yan Zhao

Keyword(s):

16S Rrna ◽

Classification Scheme ◽

Rflp Analysis ◽

Plant Diseases ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Similarity Coefficients ◽

Wide Range

Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the clustal_x program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative ‘Candidatus Phytoplasma’ taxa.

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