scholarly journals Phylogenetic Diversity of Archaea in Shallow Hydrothermal Vents of Eolian Islands, Italy

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 156 ◽  
Author(s):  
Concetta Gugliandolo ◽  
Teresa L. Maugeri
Keyword(s):  
Hydrothermal Vents ◽  
Inorganic Compounds ◽  
Archaeal Community ◽  
Hydrothermal Systems ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Vulcano Island ◽  
High Concentrations ◽  
Shallow Hydrothermal Vents ◽  
The 16S Rrna Gene

Shallow hydrothermal systems (SHS) around the Eolian Islands (Italy), related to both active and extinct volcanism, are characterized by high temperatures, high concentrations of CO2 and H2S, and low pH, prohibitive for the majority of eukaryotes which are less tolerant to the extreme conditions than prokaryotes. Archaea and bacteria are the key elements for the functioning of these ecosystems, as they are involved in the transformation of inorganic compounds released from the vent emissions and are at the basis of the hydrothermal system food web. New extremophilic archaea (thermophilic, hyperthermophilic, acidophilic, alkalophilic, etc.) have been isolated from vents of Vulcano Island, exhibiting interesting features potentially valuable in biotechnology. Metagenomic analyses, which mainly involved molecular studies of the 16S rRNA gene, provided different insights into microbial composition associated with Eolian SHS. Archaeal community composition at Eolian vent sites results greatly affected by the geochemistry of the studied vents, principally by hypersaline conditions and declining temperatures. Archaeal community in sediments was mostly composed by hyperthermophilic members of Crenarchaeota (class Thermoprotei) and Euryarchaeota (Thermococci and Methanococci) at the highest temperature condition. Mesophilic Euryarchaeota (Halobacteria, Methanomicrobia, and Methanobacteria) increased with decreasing temperatures. Eolian SHS harbor a high diversity of largely unknown archaea, and the studied vents may be an important source of new isolates potentially useful for biotechnological purposes.

scholarly journals A Novel Microbial Zearalenone Transformation through Phosphorylation

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 294
Author(s):  
Yan Zhu ◽  
Pascal Drouin ◽  
Dion Lepp ◽  
Xiu-Zhen Li ◽  
Honghui Zhu ◽  
...  
Keyword(s):  
Microbial Transformation ◽  
Acid Tolerance ◽  
Transformation Product ◽  
The United States ◽  
Corn Silage ◽  
Rrna Gene ◽  
Bacillus Spp ◽  
High Concentrations ◽  
The 16S Rrna Gene ◽  
Bacillus Strains

Zearalenone (ZEA) is a mycotoxin widely occurring in many agricultural commodities. In this study, a purified bacterial isolate, Bacillus sp. S62-W, obtained from one of 104 corn silage samples from various silos located in the United States, exhibited activity to transform the mycotoxin ZEA. A novel microbial transformation product, ZEA-14-phosphate, was detected, purified, and identified by HPLC, LC-MS, and NMR analyses. The isolate has been identified as belonging to the genus Bacillus according to phylogenetic analysis of the 16S rRNA gene and whole genome alignments. The isolate showed high efficacy in transforming ZEA to ZEA-14-phosphate (100% transformation within 24 h) and possessed advantages of acid tolerance (work at pH = 4.0), working under a broad range of temperatures (22–42 °C), and a capability of transforming ZEA at high concentrations (up to 200 µg/mL). In addition, 23 Bacillus strains of various species were tested for their ZEA phosphorylation activity. Thirteen of the Bacillus strains showed phosphorylation functionality at an efficacy of between 20.3% and 99.4% after 24 h incubation, suggesting the metabolism pathway is widely conserved in Bacillus spp. This study established a new transformation system for potential application of controlling ZEA although the metabolism and toxicity of ZEA-14-phosphate requires further investigation.

scholarly journals Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sesilje Weiss ◽  
David Taggart ◽  
Ian Smith ◽  
Kristofer M. Helgen ◽  
Raphael Eisenhofer
Keyword(s):  
Microbial Community ◽  
Reproductive Cycle ◽  
Tammar Wallaby ◽  
The Body ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Birth Canal ◽  
Gram Positive Bacteria ◽  
Rigorous Framework ◽  
The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

scholarly journals Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents

2004 ◽  
Vol 54 (1) ◽  
pp. 175-181 ◽  
Author(s):  
Costantino Vetriani ◽  
Mark D. Speck ◽  
Susan V. Ellor ◽  
Richard A. Lutz ◽  
Valentin Starovoytov
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
East Pacific ◽  
Casamino Acids ◽  
The 16S Rrna Gene

A thermophilic, anaerobic, chemolithoautotrophic bacterium was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9° 50′ N. Cells of the organism were Gram-negative, motile rods that were about 1·0 μm in length and 0·6 μm in width. Growth occurred between 60 and 80 °C (optimum at 75 °C), 0·5 and 4·5 % (w/v) NaCl (optimum at 2 %) and pH 5 and 7 (optimum at 5·5). Generation time under optimal conditions was 1·57 h. Growth occurred under chemolithoautotrophic conditions in the presence of H2 and CO2, with nitrate or sulfur as the electron acceptor and with concomitant formation of ammonium or hydrogen sulfide, respectively. Thiosulfate, sulfite and oxygen were not used as electron acceptors. Acetate, formate, lactate and yeast extract inhibited growth. No chemoorganoheterotrophic growth was observed on peptone, tryptone or Casamino acids. The genomic DNA G+C content was 54·6 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the organism was a member of the domain Bacteria and formed a deep branch within the phylum Aquificae, with Thermovibrio ruber as its closest relative (94·4 % sequence similarity). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the newly described genus Thermovibrio. The type strain is Thermovibrio ammonificans HB-1T (=DSM 15698T=JCM 12110T).

scholarly journals The Microbial Communities of Leaves and Roots Associated with Turtle Grass (Thalassia testudinum) and Manatee Grass (Syringodium filliforme) are Distinct from Seawater and Sediment Communities, but Are Similar between Species and Sampling Sites

2018 ◽  
Vol 7 (1) ◽  
pp. 4 ◽  
Author(s):  
Kelly Ugarelli ◽  
Peeter Laas ◽  
Ulrich Stingl
Keyword(s):  
Carbon Sink ◽  
Amplicon Sequencing ◽  
Thalassia Testudinum ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Carbon Cycles ◽  
Syringodium Filiforme ◽  
Turtle Grass ◽  
Shoreline Protection ◽  
The 16S Rrna Gene

Seagrasses are vital members of coastal systems, which provide several important ecosystem services such as improvement of water quality, shoreline protection, and serving as shelter, food, and nursery to many species, including economically important fish. They also act as a major carbon sink and supply copious amounts of oxygen to the ocean. A decline in seagrasses has been observed worldwide, partly due to climate change, direct and indirect human activities, diseases, and increased sulfide concentrations in the coastal porewaters. Several studies have shown a symbiotic relationship between seagrasses and their microbiome. For instance, the sulfur, nitrogen, and carbon cycles are important biochemical pathways that seem to be linked between the plant and its microbiome. The microbiome presumably also plays a key role in the health of the plant, for example in oxidizing phyto-toxic sulfide into non-toxic sulfate, or by providing protection for seagrasses from pathogens. Two of the most abundant seagrasses in Florida include Thalassia testudinum (turtle grass) and Syringodium filliforme (manatee grass), yet there is little data on the composition of the microbiome of these two genera. In this study, the microbial composition of the phyllosphere and rhizosphere of Thalassia testudinum and Syringodium filiforme were compared to water and sediment controls using amplicon sequencing of the V4 region of the 16S rRNA gene. The microbial composition of the leaves, roots, seawater, and sediment differ from one another, but are similar between the two species of seagrasses.

scholarly journals Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows

2016 ◽  
Vol 62 (6) ◽  
pp. 538-541 ◽  
Author(s):  
Marija Kaevska ◽  
Petra Videnska ◽  
Karel Sedlar ◽  
Iva Bartejsova ◽  
Alena Kralova ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Mycobacterium Avium ◽  
Mycobacterium Avium Subsp ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Bacterial Populations ◽  
Faecal Samples ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
The 16S Rrna Gene

The aim of this study was to determine possible differences in the faecal microbiota of dairy cows infected with Mycobacterium avium subsp. paratuberculosis (Johne’s disease) in comparison with noninfected cows from the same herds. Faecal samples from cows in 4 herds were tested for M. avium subsp. paratuberculosis by real-time PCR, and faecal bacterial populations were analysed by 454 pyrosequencing of the 16S rRNA gene. The most notable differences between shedding and nonshedding cows were an increase in the genus Psychrobacter and a decrease in the genera Oscillospira, Ruminococcus, and Bifidobacterium in cows infected with M. avium subsp. paratuberculosis. The present study is the first to report the faecal microbial composition in dairy cows infected with M. avium subsp. paratuberculosis.

scholarly journals Distinct microbial composition and functions in an underground high-temperature hot spring at different depths

2019 ◽  
Author(s):  
Shijie Bai ◽  
Xiaotong Peng
Keyword(s):  
High Temperature ◽  
Microbial Communities ◽  
Hot Springs ◽  
Hot Spring ◽  
Hydrogen Oxidation ◽  
Archaeal Community ◽  
Limited Area ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Different Depths

Abstract. The microbial diversity and functions of three high-temperature neutral hot springs water samples at different depths (0 m, 19 m and 58 m) were investigated based on 16S rRNA gene sequencing and a functional gene array (GeoChip 5.0). The results revealed that the bacterial communities were distinct at different depths in the hot springs. Additionally, in response to the depths, bacterial/archaeal community compositions exhibited shifts over the depth profiles. Aquificae, Alpha-proteobacteria, and Deinococcus-Thermus were the dominating phyla at 0 m, 19 m, and 58 m, respectively. Hydrogenobacter, Sphingobium, and Thermus were the most abundant genera at 0 m, 19 m, and 58 m, respectively. The phylum Thaumarchaeota was the most abundant member of the archaeal community in the samples at different hot spring depths. Functional results of the microbial communities indicated that microbial metabolic functions were mainly related to sulfur, nitrogen cycling, and hydrogen oxidation. In summary, our results demonstrated that distinct microbial communities and functions were found at different depths of hot springs in a very limited area. These findings will provide new insights into the deep-subsurface biosphere associated with terrestrial hot springs.

scholarly journals Host reproductive cycle influences the pouch microbiota of wild Southern Hairy-nosed Wombats (Lasiorhinus latifrons)

2021 ◽  
Author(s):  
Sesilje Weiss ◽  
David Taggart ◽  
Ian Smith ◽  
Kristofer M Helgen ◽  
Raphael Eisenhofer
Keyword(s):  
Microbial Community ◽  
Reproductive Cycle ◽  
Tammar Wallaby ◽  
The Body ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Birth Canal ◽  
Gram Positive Bacteria ◽  
Rigorous Framework ◽  
The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7-90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

scholarly journals Novel, Attached, Sulfur-Oxidizing Bacteria at Shallow Hydrothermal Vents Possess Vacuoles Not Involved in Respiratory Nitrate Accumulation

2004 ◽  
Vol 70 (12) ◽  
pp. 7487-7496 ◽  
Author(s):  
Karen M. Kalanetra ◽  
Sherry L. Huston ◽  
Douglas C. Nelson
Keyword(s):  
Hydrothermal Vents ◽  
Repeated Measurements ◽  
Rrna Gene ◽  
Nitrate Accumulation ◽  
Sulfur Bacteria ◽  
Physiological Properties ◽  
Large Central Vacuole ◽  
White Point ◽  
Sulfur Oxidizing ◽  
Shallow Hydrothermal Vents

ABSTRACT Novel, vacuolate sulfur bacteria occur at shallow hydrothermal vents near White Point, Calif. There, these filaments are attached densely to diverse biotic and abiotic substrates and extend one to several centimeters into the surrounding environment, where they are alternately exposed to sulfidic and oxygenated seawater. Characterizations of native filaments collected from this location indicate that these filaments possess novel morphological and physiological properties compared to all other vacuolate bacteria characterized to date. Attached filaments, ranging in diameter from 4 to 100 μm or more, were composed of cylindrical cells, each containing a thin annulus of sulfur globule-filled cytoplasm surrounding a large central vacuole. A near-complete 16S rRNA gene sequence was obtained and confirmed by fluorescent in situ hybridization to be associated only with filaments having a diameter of 10 μm or more. Phylogenetic analysis indicates that these wider, attached filaments form within the gamma proteobacteria a monophyletic group that includes all previously described vacuolate sulfur bacteria (the genera Beggiatoa, Thioploca, and Thiomargarita) and no nonvacuolate genera. However, unlike for all previously described vacuolate bacteria, repeated measurements of cell lysates from samples collected over 2 years indicate that the attached White Point filaments do not store internal nitrate. It is possible that these vacuoles are involved in transient storage of oxygen or contribute to the relative buoyancy of these filaments.

scholarly journals Spatial and temporal constraints on the composition of microbial communities in subsurface boreholes of the Edgar Experimental Mine

2021 ◽  
Author(s):  
Patrick H. Thieringer ◽  
Alexander S. Honeyman ◽  
John R. Spear
Keyword(s):  
Microbial Communities ◽  
Spatial Scales ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Surface Hydrology ◽  
Microbial Composition ◽  
16S Rrna Gene Analysis ◽  
High Concentrations ◽  
Recharge Rates

The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. While numerous novel microbial members with unique physiological modifications remain to be identified, even greater attention is required to understand the near-subsurface and its continuity with surface systems. This raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular biological and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine (~150 meters below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric water feeding boreholes demonstrated variable recharge rates due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Proteobacteria, Firmicutes, and Nanoarcheota associated with endemic subsurface communities. Two other boreholes presented sequences related to soil-originating microbiota, which likely indicate a direct link to surface infiltration. High concentrations of sulfate suggest sulfur-related metabolic strategies dominate within these near-subsurface boreholes. Overall, results indicate microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments.

scholarly journals 247 The effect of diet on the microbial community structure and composition in lactating Jersey cows consuming a mixture of straw and dry distillers grains plus solubles in replacement of alfalfa hay

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 138-139
Author(s):  
Allison Knoell ◽  
Nirosh Aluthge ◽  
Waseem Abbas ◽  
Alison Bartenslager ◽  
Jared Judy ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dry Matter ◽  
Archaeal Community ◽  
Distillers Grains ◽  
Rrna Gene ◽  
Alfalfa Hay ◽  
Jersey Cows ◽  
The 16S Rrna Gene

Abstract The rumen microbial community is responsible for producing a majority of the energetic needs for the animal, yet our understanding of the rumen microbiome is in its infancy. To better understand the effect of corn-ethanol coproducts on rumen microbial communities, a replicated 4 × 4 Latin square design study utilizing 12 cows in three squares was conducted to evaluate the replacement of alfalfa hay with a mixture (CoP) containing straw and dried distillers grains plus solubles (DDGS) in lactating Jersey cows. The experimental treatments were (proportions on a dry matter basis): a control diet (CON) containing 18.2% of alfalfa hay with no straw or DDGS. A low coproduct diet (LCoP) containing 12.1% alfalfa, 2.1% straw, and 6.0% DDGS. A medium coproduct diet (MCoP) containing 6.1% alfalfa, 4.2% straw, and 12.1% DDGS. A high coproduct diet (HCoP) containing 6.2% straw, 18.1% DDGS with no alfalfa. Rumen digesta samples were collected via an esophageal tube. No differences were observed for milk production and dry matter intake (P ≥ 0.307) (mean ± SEM) 19.5 kg ± 0.60, 29.6 kg ± 0.91, across treatments, while a decrease in methane was observed (P &lt; 0.01) for the HCoP treatment. The bacterial community was assessed by sequencing the V4 region of the 16S rRNA gene. Additionally, the archaeal community was assessed by sequencing the V4-V5 region of the 16S rRNA gene on the Illumina MiSeq platform. Amplicon Sequence Variants were identified using the DADA2 pipeline. No significant differences were observed for the bacterial (P = 0.334) and archaeal (P = 0.593) communities. Although global effects in microbial community dynamics were not observed, differential taxa were observed with Lachnospiraceae being the major differentially abundant Family. The archaeal community composition demonstrated that Methanobacteriales to be the differentially abundant Order across treatments, and may contribute to methane production.

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