scholarly journals Temperature and elemental sulfur shape microbial communities in two extremely acidic aquatic volcanic environments

2020 ◽  
Author(s):  
Diego Rojas-Gätjens ◽  
Alejandro Arce-Rodríguez ◽  
Fernando Puente-Sánchez ◽  
Roberto Avendaño ◽  
Eduardo Libby ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Elemental Sulfur ◽  
River System ◽  
Low Ph ◽  
Rrna Gene ◽  
Mountain Range ◽  
Volcanic Origin ◽  
Poas Volcano ◽  
Sulfur Oxidizing ◽  
High Sulfate

Aquatic environments of volcanic origin provide an exceptional opportunity to study the adaptations of microbial communities to early planet life conditions such as high temperatures, high metal concentrations, and low pH. Here, we characterized the prokaryotic communities and physicochemical properties of seepage sites at the bottom of the Poas Volcano crater and the Agrio River, two geologically related extremely acidic environments located in the Central Volcanic mountain range of Costa Rica. Both locations hold a very low pH (pH 1.79−2.20) and have high sulfate and iron concentrations (Fe = 47−206 mg/L, SO42- = 1170-2460 mg/L measured as S), but significant differences in their temperature (90.0−95.0°C in the seepages at Poas Volcano versus 19.1−26.6 °C in Agrio River) and in the abundance of elemental sulfur. Based on the analysis of 16S rRNA gene sequences, we determined that Sulfobacillus spp., sulfur-oxidizing bacteria, represented more than half (58.4−78.4%) of the sequences in Poas Volcano seepage sites, while Agrio River was dominated by the iron− and sulfur−oxidizing Leptospirillum (7.4−55.5%) and members of the archeal order Thermoplasmatales (16.0−58.2%). Both environments share some chemical characteristics and part of their microbiota, however the temperature and the presence of reduced sulfur are likely the main distinguishing feature ultimately shaping their microbial communities. Our data suggest that in the Poas Volcano-Agrio River system there is a common metabolism but with specialization of species that adapt to the physicochemical conditions of each environment.

Sulfurovum indicum sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal plume in the Northwestern Indian Ocean

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Shaobin Xie ◽  
Shasha Wang ◽  
Dengfeng Li ◽  
Zongze Shao ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
Indian Ocean ◽  
Deep Sea ◽  
Type Species ◽  
Elemental Sulfur ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Sulfur Oxidizing

A novel mesophilic, hydrogen-, and sulfur-oxidizing bacterium, designated strain ST-419T, was isolated from a deep-sea hydrothermal vent plume on the Carlsberg Ridge of the Northwestern Indian Ocean. The isolate was a Gram-staining-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 4–50 °C (optimum 37 °C), pH 5.0–8.6 (optimum pH 6.0) and 1.0–5.0 % (w/v) NaCl (optimum 3.0 %). ST-419T could grow chemlithoautotrophically with molecular hydrogen, sulfide, elemental sulfur and thiosulfate as energy sources. Molecular oxygen, nitrate and elemental sulfur could be used as electron acceptors. The predominant fatty acids were C16 : 1ω7c, C18 : 1ω7c and C16 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The respiratory quinone was menaquinone MK-6 and the G+C content of the genomic DNA was 42.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that ST-419T represented a member of genus Sulfurovum and was most closely related to Sulfurovum riftiae 1812ET, with 97.6 % sequence similarity. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between ST-419T and S. riftiae 1812ET were 74.6 and 19.6 %, respectively. The combined genotypic and phenotypic data indicate that ST-419T represents a novel species within the genus Sulfurovum , for which the name Sulfurovum indicum sp. nov. is proposed. The type strain is ST-419T (=MCCC 1A17954T=KCTC 25164T).

scholarly journals Isolation, Characterization, and In Situ Detection of a Novel Chemolithoautotrophic Sulfur-Oxidizing Bacterium in Wastewater Biofilms Growing under Microaerophilic Conditions

2004 ◽  
Vol 70 (5) ◽  
pp. 3122-3129 ◽  
Author(s):  
Tsukasa Ito ◽  
Kenichi Sugita ◽  
Satoshi Okabe
Keyword(s):  
Laser Scanning ◽  
Elemental Sulfur ◽  
Sulfur Cycle ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Rrna Gene ◽  
Effective Measure ◽  
Sulfur Oxidizing ◽  
Microaerophilic Conditions

ABSTRACT We successfully isolated a novel aerobic chemolithotrophic sulfur-oxidizing bacterium, designated strain SO07, from wastewater biofilms growing under microaerophilic conditions. For isolation, the use of elemental sulfur (S0), which is the most abundant sulfur pool in the wastewater biofilms, as the electron donor was an effective measure to establish an enrichment culture of strain SO07 and further isolation. 16S rRNA gene sequence analysis revealed that newly isolated strain SO07 was affiliated with members of the genus Halothiobacillus, but it was only distantly related to previously isolated species (89% identity). Strain SO07 oxidized elemental sulfur, thiosulfate, and sulfide to sulfate under oxic conditions. Strain SO07 could not grow on nitrate. Organic carbons, including acetate, propionate, and formate, could not serve as carbon and energy sources. Unlike other aerobic sulfur-oxidizing bacteria, this bacterium was sensitive to NaCl; growth in medium containing more than 150 mM was negligible. In situ hybridization combined with confocal laser scanning microscopy revealed that a number of rod-shaped cells hybridized with a probe specific for strain SO07 were mainly present in the oxic biofilm strata (ca. 0 to 100 μm) and that they often coexisted with sulfate-reducing bacteria in this zone. These results demonstrated that strain SO07 was one of the important sulfur-oxidizing populations involved in the sulfur cycle occurring in the wastewater biofilm and was primarily responsible for the oxidation of H2S and S0 to SO4 2− under oxic conditions.

scholarly journals Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1511 ◽  
Author(s):  
Florent E. Angly ◽  
Candice Heath ◽  
Thomas C. Morgan ◽  
Hemerson Tonin ◽  
Virginia Rich ◽  
...  
Keyword(s):  
Water Quality ◽  
Great Barrier Reef ◽  
Microbial Communities ◽  
River Mouth ◽  
Environmental Parameters ◽  
River System ◽  
Rrna Gene ◽  
Barrier Reef ◽  
Wet Season ◽  
Marine Microbial Communities

The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR), with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae) and Synechococcales (e.g.,Prochlorococcus), and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010–11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics.

scholarly journals Thiovirga sulfuroxydans gen. nov., sp. nov., a chemolithoautotrophic sulfur-oxidizing bacterium isolated from a microaerobic waste-water biofilm

2005 ◽  
Vol 55 (3) ◽  
pp. 1059-1064 ◽  
Author(s):  
Tsukasa Ito ◽  
Kenichi Sugita ◽  
Isao Yumoto ◽  
Yoshinobu Nodasaka ◽  
Satoshi Okabe
Keyword(s):  
Waste Water ◽  
Electron Acceptor ◽  
New Genus ◽  
Elemental Sulfur ◽  
Physiological Data ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Terminal Electron Acceptor ◽  
Optimum Ph ◽  
Sulfur Oxidizing

A novel mesophilic, chemolithoautotrophic, sulfur-oxidizing bacterium, designated strain SO07T, was isolated from a microaerobic waste-water biofilm. Chemolithoautotrophic growth was observed with elemental sulfur, sulfide and thiosulfate as sole electron donors and oxygen as electron acceptor. Anaerobic and heterotrophic growth were not observed. Nitrate was not used as a terminal electron acceptor. The optimum pH and temperature for growth were pH 7·5 and 30 °C, respectively. The major isoprenoid quinone was Q-8. The DNA G+C content of strain SO07T was 47·1 mol%. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain SO07T formed a monophyletic group in the γ-Proteobacteria with only 89 % similarity to members of the genus Halothiobacillus, its nearest phylogenetic neighbours. In addition, the isolate differed from members of the genus Halothiobacillus in its requirement for and tolerance of NaCl; strain SO07T was unable to grow in NaCl concentrations of more than 180 mM. On the basis of phylogenetic, chemotaxonomic and physiological data, it is proposed that isolate SO07T (=JCM 12417T=ATCC BAA-1033T) represents the type strain of a novel species in a new genus, Thiovirga sulfuroxydans gen. nov., sp. nov.

scholarly journals Effects of Ocean Acidification, Hypoxia, and Warming on the Gut Microbiota of the Thick Shell Mussel Mytilus coruscus Through 16S rRNA Gene Sequencing

2021 ◽  
Vol 8 ◽  
Author(s):  
Fahim Ullah Khan ◽  
Yueyong Shang ◽  
Xueqing Chang ◽  
Hui Kong ◽  
Amina Zuberi ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Ocean Acidification ◽  
Microbial Communities ◽  
16S Rrna Gene Sequencing ◽  
Low Ph ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Mytilus Coruscus ◽  
Marine Mussels

Gut microbiota play a very important role in the health of the host, such as protecting from pathogens and maintaining homeostasis. However, environmental stressors, such as ocean acidification, hypoxia, and warming can affect microbial communities by causing alteration in their structure and relative abundance and by destroying their network. The study aimed to evaluate the combined effects of low pH, low dissolved oxygen (DO) levels, and warming on gut microbiota of the mussel Mytilus coruscus. Mussels were exposed to two pH levels (8.1, 7.7), two DO levels (6, 2 mg L−1), and two temperature levels (20, 30°C) for a total of eight treatments for 30 days. The experiment results showed that ocean acidification, hypoxia, and warming affected the community structure, species richness, and diversity of gut microbiota. The most abundant phyla noted were Proteobacteria, Bacteroidetes, and Firmicutes. Principal coordinate analysis (PCoA) revealed that ocean acidification, hypoxia, and warming change microbial community structure. Low pH, low DO, and increased temperature can cause shifting of microbial communities toward pathogen dominated microbial communities. Linear discriminant analysis effect size (LEfSe) showed that the significantly enriched biomarkers in each group are significantly different at the genus level. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis revealed that the gut microbiome of the mussels is associated with many important functions, such as amino acid transport and metabolism, transcription, energy production and conservation, cell wall, membrane and envelope biogenesis, and other functions. This study highlights the complexity of interaction among pH, DO, and temperature in marine organisms and their effects on the gut microbiota and health of marine mussels.

scholarly journals Sedimenticola thiotaurini sp. nov., a sulfur-oxidizing bacterium isolated from salt marsh sediments, and emended descriptions of the genus Sedimenticola and Sedimenticola selenatireducens

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2522-2530 ◽  
Author(s):  
Beverly E. Flood ◽  
Daniel S. Jones ◽  
Jake V. Bailey
Keyword(s):  
Salt Marsh ◽  
Elemental Sulfur ◽  
Carbon Fixation ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Separate Species ◽  
Sulfur Oxidizing ◽  
Marsh Sediments ◽  
Salt Marsh Sediments ◽  
Sulfur Inclusions

A marine facultative anaerobe, strain SIP-G1T, was isolated from salt marsh sediments, Falmouth, MA, USA. Phylogenetic analysis of its 16S rRNA gene sequence indicated that it belongs to an unclassified clade of Gammaproteobacteria that includes numerous sulfur-oxidizing bacteria that are endosymbionts of marine invertebrates endemic to sulfidic habitats. Strain SIP-G1T is a member of the genus Sedimenticola, of which there is one previously described isolate, Sedimenticola selenatireducens AK4OH1T. S. selenatireducens AK4OH1T was obtained for further characterization and comparison with strain SIP-G1T. The two strains were capable of coupling the oxidation of thiosulfate, tetrathionate, elemental sulfur and sulfide to autotrophic growth and they produced sulfur inclusions as metabolic intermediates. They showed varying degrees of O2 sensitivity, but when provided amino acids or peptides as a source of energy, they appeared more tolerant of O2 and exhibited concomitant production of elemental sulfur inclusions. The organic substrate preferences and limitations of these two organisms suggest that they possess an oxygen-sensitive carbon fixation pathway(s). Organic acids may be used to produce NADPH through the TCA cycle and are used in the formation of polyhydroxyalkanoates. Cell-wall-deficient morphotypes appeared when organic compounds (especially acetate) were present in excess and reduced sulfur was absent. Levels of DNA–DNA hybridization (∼47 %) and phenotypic characterization indicate that strain SIP-G1T represents a separate species within the genus Sedimenticola, for which the name Sedimenticola thiotaurini sp. nov. is proposed. The type strain is SIP-G1T ( = ATCC BAA-2640T = DSM 28581T). The results also justify emended descriptions of the genus Sedimenticola and of S. selenatireducens.

scholarly journals A Comparative Study on the Microbial Communities of Rhynchophorus ferrugineus (Red Palm Weevil)-Infected and Healthy Palm Trees

2021 ◽  
Author(s):  
N. Alshammari ◽  
Meshari Alazmi ◽  
Naimah A. Alanazi ◽  
Abdel Moneim E. Sulieman ◽  
Vajid N. Veettil ◽  
...  
Keyword(s):  
Microbial Communities ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rhynchophorus Ferrugineus ◽  
Tree Trunk ◽  
Red Palm Weevil ◽  
Healthy Tree ◽  
Palm Trees ◽  
Infected Tree ◽  
Palm Weevil

AbstractSeveral studies have investigated palm trees’ microbiota infected with red palm weevil (RPW) (Rhynchophorus ferrugineus), the major pest of palm trees. This study compared the microbial communities of infected and uninfected palm trees in the Hail region, Northern Saudi Arabia, determined by high-throughput 16S rRNA gene sequencing by Illumina MiSeq. The results indicated that taxonomic diversity variation was higher for infected tree trunk than the healthy tree trunk. Soil samples from the vicinity of healthy and infected trees did not have a significant variation in bacterial diversity. Myxococcota, Acidobacteriota, and Firmicutes were the dominant phyla in RPW-infected tree trunk, and Pseudomonadaceae was the most prominent family. This study is the first report on the characterization of RPW-infected and healthy palm trees’ microbiome.

scholarly journals Structure of Microbial Communities When Complementary Effluents Are Anaerobically Digested

2021 ◽  
Vol 11 (3) ◽  
pp. 1293
Author(s):  
Ana Eusébio ◽  
André Neves ◽  
Isabel Paula Marques
Keyword(s):  
Anaerobic Digestion ◽  
Microbial Communities ◽  
Volatile Fatty Acids ◽  
Olive Mill Wastewater ◽  
Organic Load ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Olive Mill

Olive oil and pig productions are important industries in Portugal that generate large volumes of wastewater with high organic load and toxicity, raising environmental concerns. The principal objective of this study is to energetically valorize these organic effluents—piggery effluent and olive mill wastewater—through the anaerobic digestion to the biogas/methane production, by means of the effluent complementarity concept. Several mixtures of piggery effluent were tested, with an increasing percentage of olive mill wastewater. The best performance was obtained for samples of piggery effluent alone and in admixture with 30% of OMW, which provided the same volume of biogas (0.8 L, 70% CH4), 63/75% COD removal, and 434/489 L CH4/kg SVin, respectively. The validation of the process was assessed by molecular evaluation through Next Generation Sequencing (NGS) of the 16S rRNA gene. The structure of the microbial communities for both samples, throughout the anaerobic process, was characterized by the predominance of bacterial populations belonging to the phylum Firmicutes, mainly Clostridiales, with Bacteroidetes being the subdominant populations. Archaea populations belonging to the genus Methanosarcina became predominant throughout anaerobic digestion, confirming the formation of methane mainly from acetate, in line with the greatest removal of volatile fatty acids (VFAs) in these samples.

scholarly journals Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shenzheng Zeng ◽  
Sukontorn Khoruamkid ◽  
Warinphorn Kongpakdee ◽  
Dongdong Wei ◽  
Lingfei Yu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Well Being ◽  
Pacific White Shrimp ◽  
Shrimp Farming ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Shrimp Culture ◽  
Water And Sediment ◽  
Surrounding Environment ◽  
Shrimp Production

Abstract The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The “Aquamimicry system”, mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

scholarly journals Microbial drivers of methane emissions from unrestored industrial salt ponds

2021 ◽  
Author(s):  
Jinglie Zhou ◽  
Susanna M. Theroux ◽  
Clifton P. Bueno de Mesquita ◽  
Wyatt H. Hartman ◽  
Ye Tian ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Flux ◽  
Methane Emissions ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Salt Ponds ◽  
Salt Pond ◽  
Reference Wetlands ◽  
Reference Wetland ◽  
The Impact

AbstractWetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

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