Comprehensive Longitudinal Analysis of the Five Sisters Hot Springs in Yellowstone National Park Reveals a Dynamic Thermoalkaline Environment

Abstract Research focused on microbial populations of thermoalkaline springs has been driven in a large part by the lure of discovering functional enzymes with industrial applications in high-pH and high temperature environments. However, the fundamental ecology of these springs has largely been overlooked. To better understand the functional outcomes of interactions between the geochemistry and the microbial community of thermoalkaline springs, we conducted a three-year study of the Five Sisters (FS) springs that included high-resolution geochemical measurements, 16S rRNA sequencing of the bacterial and archaeal community, and mass spectrometry based extracellular and intracellular small molecule characterization. By combining all four datasets, we completed a comprehensive analysis of the intricate thermoalkaline spring system. Over the course of the study, the microbial population responded to changing environmental conditions, with archaeal populations decreasing in both relative abundance and diversity when compared to bacterial populations. Decreases in the relative abundance of Archaea were associated with environmental changes that included decreased availability of specific nitrogen and sulfur containing extracellular small molecules. The multi-factorial analysis suggests a complex and dynamic environment with an elastic microbial community that responded to geochemical and extracellular small molecule transitions.

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Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment

Archaea ◽

10.1155/2018/9319345 ◽

2018 ◽

Vol 2018 ◽

pp. 1-12 ◽

Cited By ~ 1

Author(s):

Xiu-lu Lang ◽

Xiang Chen ◽

Ai-ling Xu ◽

Zhi-wen Song ◽

Xin Wang ◽

...

Keyword(s):

Microbial Community ◽

Constructed Wetlands ◽

Relative Abundance ◽

Constructed Wetland ◽

Free Surface Flow ◽

Archaeal Community ◽

Illumina Miseq ◽

Surface Flow ◽

Community Structures ◽

Soil And Water

Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Proteobacteria were the dominant bacteria, making up 35.38%~48.66% relative abundance. Euryarchaeotic were the absolute dominant archaea in the influent sample with the relative abundance of 93.29%, while Thaumarchaeota showed dominance in the other three samples, making up 50.58%~75.70%. The relative abundances of different species showed great changes in bacteria and archaea, and the number of dominant species in bacteria was much higher than that in archaea. Compared to archaea, the community compositions of bacteria were more abundant and the changes were more significant. Meanwhile, bacteria and archaea had large differences in compositions between water and soil. The microbial richness in water was significantly higher than that in soil. Simultaneously, soil had a significant enrichment effect on some microbial flora.

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The diversity of plankton as bioindicators in Kakap River Estuary, West Kalimantan

DEPIK ◽

10.13170/depik.10.2.21303 ◽

2021 ◽

Vol 10 (2) ◽

pp. 174-179

Author(s):

Widadi Padmarsari Soetignya ◽

Patrisia Marniati ◽

Mardan Adijaya ◽

Yunita Magrima Anzani

Keyword(s):

Relative Abundance ◽

Environmental Changes ◽

Diversity Index ◽

River Estuary ◽

West Kalimantan ◽

Abundance And Diversity ◽

Index Value ◽

Plankton Diversity ◽

Research Period

Kakap River Estuary plays an essential role in the life organisms, but it is vulnerable to environmental changes and pollution caused by human activities. This study aims to assess the presence of plankton species, their abundance and diversity as aquatic ecological bio-indicators in Kakap River Estuary. Plankton and water samples were taken for three months, with a frequency of one sample per month, viz. in March, April and June 2020 from four sampling stations in Kakap River Estuary, West Kalimantan. A total of 34 species of plankton were observed from all sampling sites, and identified to belong to 18 classes. Chlorophyceae had the highest relative abundance among the phytoplanktons (40.10%), followed by Bacillariophyceae (21.86%) and Cyanophyceae (19.28%). Oscillatoria sp. and Hydrodictyon sp. were the most dominant phytoplankton species. There were 8 classes of zooplankton identified from all sampling stations throughout the research period. Hexanauplia had the highest relative abundance among the zooplanktons (36.56%) followed by Euglenophyceae (24.37%). The plankton diversity index (H ′) values ranged between 2.33 -3.11. The plankton evenness index value ranged from 0.79 to 0.89 which indicates high plankton evenness at all samping stations, and this is supported by a low dominance index value at all stations ranging from 0.06-0.16. Station 1 had high Shannon-Wienner diversity index score, while for station 2, 3, 4, their scores were in the moderate level. Overall. the diversity index of the plankton from all sampling sites indicated that the quality of the water had no pollution to light pollution level.Keywords:PhytoplanktonZooplanktonWater quality

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Dynamics of a Pig Slurry Microbial Community during Anaerobic Storage and Management

Applied and Environmental Microbiology ◽

10.1128/aem.72.5.3578-3585.2006 ◽

2006 ◽

Vol 72 (5) ◽

pp. 3578-3585 ◽

Cited By ~ 88

Author(s):

Pascal Peu ◽

Hubert Brugï¿½re ◽

Anne-Marie Pourcher ◽

Monique Kï¿½rourï¿½dan ◽

Jean-Jacques Godon ◽

...

Keyword(s):

Microbial Community ◽

Archaeal Community ◽

Single Strand Conformation Polymorphism ◽

16S Rrna Genes ◽

Rrna Genes ◽

Pig Slurry ◽

Bacterial Populations ◽

Cultural Methods ◽

Total Dna ◽

Anaerobic Storage

ABSTRACT The microbial community of a pig slurry on a farm was monitored for 6 months using both molecular and cultural approaches. Sampling was carried out at all the different stages of effluent handling, from the rearing build-up to slurry spreading. Total DNA of each sample was extracted and analyzed by PCR-single-strand conformation polymorphism (SSCP) analysis using primers targeting the 16S rRNA genes from the archaeal and bacterial domains and also the Eubacterium-Clostridium, Bacillus-Streptococcus-Lactobacillus, and Bacteroides-Prevotella groups. A comparison of the SSCP profiles showed that there were rapid changes in the dominant bacterial community during the first 2 weeks of anaerobic storage and that the community was relatively stable thereafter. Several bacterial populations, identified as populations closely related to uncultured Clostridium and Porphyromonas and to Lactobacillus and Streptococcus cultured species commonly isolated from pig feces, remained present and dominant from the rearing build-up to the time of spreading. Enumeration of fecal indicators (enterococci and Escherichia coli) performed in parallel using cultural methods revealed the same trends. On the other hand, the archaeal community adapted slowly during pig slurry storage, and its diversity increased. A shift between two hydrogenotrophic methanogenic Methanobrevibacter populations from the storage pit to the pond was observed. Microorganisms present in pig slurry at the time of spreading could not be detected in soil after spreading by either molecular or cultural techniques, probably because of the detection limit inherent in the two techniques.

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Impacts of Mootral on Methane Production, Rumen Fermentation, and Microbial Community in an in vitro Study

Frontiers in Veterinary Science ◽

10.3389/fvets.2020.623817 ◽

2021 ◽

Vol 7 ◽

Author(s):

Eslam Ahmed ◽

Rintaro Yano ◽

Miho Fujimori ◽

Deepashree Kand ◽

Masaaki Hanada ◽

...

Keyword(s):

Microbial Community ◽

Relative Abundance ◽

Methane Production ◽

Statistical Significance ◽

Archaeal Community ◽

Rumen Fermentation ◽

Mitigation Strategies ◽

Dependent Manner ◽

Dose Dependent

Methane mitigation strategies have a two-sided benefit for both environment and efficient livestock production. This preliminary short-term in vitro trial using Mootral (garlic and citrus extracts), a novel natural feed supplement, was conducted to evaluate its efficacy on rumen fermentation characteristics, methane production, and the bacterial and archaeal community. The experiment was performed as a batch culture using rumen fluid collected from sheep, and Mootral was supplemented in three concentrations: 0% (Control), 10%, and 20% of the substrate (50% Grass:50% Concentrate). The rumen fermentation data and alpha diversity of microbial community were analyzed by ordinary one-way analysis of variance. The relative abundance and statistical significance of families and operational taxonomic units (OTUs) among the groups were compared by Kruskal–Wallis H test using Calypso software. After 24-h incubation at 39°C, Mootral in a dose-dependent manner improved the production of total volatile fatty acids and propionate while it reduced the acetate proportion and acetate/propionate ratio. The total produced gas was two times higher in the Mootral-supplemented groups than control (P < 0.01), while the proportion of methane in the produced gas was reduced by 22% (P < 0.05) and 54% (P < 0.01) for 10 and 20% Mootral, respectively. Mootral did not change pH, digestibility, and ammonia-nitrogen. Microbial community analyses showed that Mootral effectively changed the ruminal microbiome. The bacterial community showed an increase of the relative abundance of the propionate-producing family such as Prevotellaceae (P = 0.014) and Veillonellaceae (P = 0.030), while there was a decrease in the relative abundance of some hydrogen-producing bacteria by Mootral supplementation. In the archaeal community, Methanobacteriaceae was decreased by Mootral supplementation compared with control (P = 0.032), while the Methanomassiliicoccaceae family increased in a dose-dependent effect (P = 0.038). The results of the study showed the efficacy of the new mixture to alter the ruminal microbial community, produce more propionate, and reduce microbial groups associated with methane production, thus suggesting that Mootral is a promising natural mixture for methane reduction from ruminants.

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Weaning Age Affects the Development of the Ruminal Bacterial and Archaeal Community in Hu Lambs During Early Life

Frontiers in Microbiology ◽

10.3389/fmicb.2021.636865 ◽

2021 ◽

Vol 12 ◽

Author(s):

Huiling Mao ◽

Yanfang Zhang ◽

Yan Yun ◽

Wenwen Ji ◽

Zhao Jin ◽

...

Keyword(s):

Microbial Community ◽

Relative Abundance ◽

Age Groups ◽

Lactate Concentration ◽

Archaeal Community ◽

Milk Replacer ◽

Significant Difference ◽

Weaning Age ◽

Bacterial And Archaeal Communities ◽

Positive Correlations

Weaning plays an important role in many animal processes, including the development of the rumen microbiota in ruminants. Attaining a better understanding of the development of the rumen microbial community at different weaning stages can aid the identification of the optimal weaning age. We investigated the effects of weaning age on ruminal bacterial and archaeal communities in Hu lambs. Thirty male Hu lambs were randomly assigned to two weaning-age groups: a group weaned at 30 days of age (W30) and a group weaned at 45 days of age (W45), with each group having five replicate pens. On the weaning day (day 30 for W30 and day 45 for W45) and at 5 days postweaning [day 35 for W30 (PW30) and day 50 for W45 (PW45)], one lamb from each replicate was randomly selected and sacrificed. Rumen contents were collected to examine the ruminal microbiota. Compared to W30, PW30 had a decreased relative abundance of Bacteroidetes. At genus level, the extended milk replacer feeding (W45 vs. W30) increased the relative abundance of Ruminococcus while decreased that of Prevotella and Dialister. Compared to W30, PW30 exhibited decreased relative abundances of Prevotella, Dialister and Bacteroides but an increased unclassified Coriobacteriaceae. No significant difference was noted in the detected archaeal taxa among the animals. The function “biosynthesis of secondary metabolites” was less predominant in PW30 than in W30, whereas the opposite held true for “metabolism of cofactors and vitamins.” Some bacterial genera were significantly correlated with rumen volatile fatty acid (VFA) concentration or other animal measures, including negative correlations between ruminal VFA concentration and unclassified Mogibacteriaceae and unclassified Veillonellaceae; positive correlations of ruminal papillae length with Fibrobacter and unclassified Lachnospiraceae, but negative correlations with Mitsuokella and Succiniclasticum; and negative correlations between plasma D-lactate concentration and Prevotella, unclassified Paraprevotellaceae, and Desulfovibrio. Our results revealed that the ruminal bacterial community underwent larger changes over time in lambs weaned at 30 days of age than in lambs weaned half a month later. Thus, extending milk replacer feeding to 45 days weaning was recommended from the perspective of the rumen microbial community in the Hu lamb industry.

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Metagenomics Uncovers a Core SAR11 Population in Brackish Surface Waters of the Baltic Sea

Water ◽

10.3390/w12020501 ◽

2020 ◽

Vol 12 (2) ◽

pp. 501 ◽

Cited By ~ 2

Author(s):

Poorna Vidanage ◽

Seok-Oh Ko ◽

Seungdae Oh

Keyword(s):

Baltic Sea ◽

Relative Abundance ◽

Surface Waters ◽

Environmental Changes ◽

Rrna Gene ◽

The Baltic Sea ◽

Bacterial Populations ◽

The Core ◽

The Baltic ◽

Seasonal Shifts

The Baltic Sea represents one of the largest brackish ecosystems where various environmental factors control dynamic seasonal shifts in the structure, diversity, and function of the planktonic microbial communities. In this study, despite seasonal fluctuations, several bacterial populations (<2% of the total OTUs) that are highly dominant (25% of relative abundance) and highly frequently occurring (>85% of occurrence) over four seasons were identified. Mathematical models using occurrence frequency and relative abundance data were able to describe community assembly persisting over time. Further, this work uncovered one of the core bacterial populations phylogenetically affiliated to SAR11 subclade IIIa. The analysis of the hypervariable region of 16S rRNA gene and single copy housekeeping genes recovered from metagenomic datasets suggested that the population was unexpectedly evolutionarily closely related to those inhabiting a mesosaline lacustrine ecosystem rather than other marine/coastal members. Our metagenomic results further revealed that the newly-identified population was the major driver facilitating the seasonal shifts in the overall community structure over the brackish waters of the Baltic Sea. The core community uncovered in this study supports the presence of a brackish water microbiome distinguishable from other marine and freshwater counterparts and will be a useful sentinel for monitoring local/global environmental changes posed on brackish surface waters.

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Interplay between eutrophication and climate warming on bacterial communities in coastal sediments differs depending on water depth and oxygen history

Scientific Reports ◽

10.1038/s41598-021-02725-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Laura Seidel ◽

Elias Broman ◽

Stephanie Turner ◽

Magnus Ståhle ◽

Mark Dopson

Keyword(s):

Relative Abundance ◽

Water Depth ◽

Bacterial Communities ◽

Environmental Changes ◽

Organic Matter Content ◽

Matter Content ◽

Coastal Sediments ◽

Rrna Gene ◽

Low Oxygen ◽

Bacterial Populations

AbstractCoastal aquatic systems suffer from nutrient enrichment, which results in accelerated eutrophication effects due to increased microbial metabolic rates. Climate change related prolonged warming will likely accelerate existing eutrophication effects, including low oxygen concentrations. However, how the interplay between these environmental changes will alter coastal ecosystems is poorly understood. In this study, we compared 16S rRNA gene amplicon based bacterial communities in coastal sediments of a Baltic Sea basin in November 2013 and 2017 at three sites along a water depth gradient with varying bottom water oxygen histories. The shallow site showed changes of only 1.1% in relative abundance of bacterial populations in 2017 compared to 2013, while the deep oxygen-deficient site showed up to 11% changes in relative abundance including an increase of sulfate-reducing bacteria along with a 36% increase in organic matter content. The data suggested that bacterial communities in shallow sediments were more resilient to seasonal oxygen decline, while bacterial communities in sediments subjected to long-term hypoxia seemed to be sensitive to oxygen changes and were likely to be under hypoxic/anoxic conditions in the future. Our data demonstrate that future climate changes will likely fuel eutrophication related spread of low oxygen zones.

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Maize (Zea mays L.) Seedlings Rhizosphere Microbial Community as Responded to Acidic Biochar Amendment Under Saline Conditions

Frontiers in Microbiology ◽

10.3389/fmicb.2021.789235 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mukesh Kumar Soothar ◽

Abdoul Kader Mounkaila Hamani ◽

Muhammad Fahad Sardar ◽

Mahendar Kumar Sootahar ◽

Yuanyuan Fu ◽

...

Keyword(s):

Microbial Community ◽

Microbial Biomass ◽

Relative Abundance ◽

Soil Microbial Biomass ◽

Bacterial Abundance ◽

Principal Component ◽

Alpha Diversity ◽

Maize Seedlings ◽

Soil Microbial ◽

Abundance And Diversity

Biochar has extensively been used for multiple purposes in agriculture, including improving soil microbial biomass. The current study aimed to investigate the effect of acidic biochar on maize seedlings’ rhizosphere bacterial abundance under salinity. There were seven treatments and three replicates in a controlled greenhouse coded as B0S1, B1S1, and B2S1 and B0S2, B1S2, and B2S2. CK is control (free of biochar and salt); B0, B1, and B2 are 0, 15, and 30 g biochar (kg soil)–1; and S1 and S2 are 2.5 and 5 g salt pot–1 that were amended, respectively. After harvesting the maize seedlings, the soil samples were collected and analyzed for soil microbial biomass, bacterial abundance, and diversity. The results revealed that relative abundance of Proteobacteria, Actinobacteria, and Chloroflexi increased on phylum level, whereas Actinomarinales, Alphaproteobacteria, and Streptomyces enhanced on genus level, respectively, in B2S1 and B2S2, when compared with CK and non-biochar amended soil under saline conditions. The relative abundance of Actinomarinales was positively correlated with total potassium (TK) and Gematimonadetes negatively correlated with total phosphorus (TP). Biochar addition slightly altered the Ace1, Chao1, and alpha diversity. Principal component analysis corresponded to the changes in soil bacterial community that were closely associated with biochar when compared with CK and salt-treated soils. In conclusion, acidic biochar showed an improved soil microbial community under salinity.

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The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs

Animals ◽

10.3390/ani11072139 ◽

2021 ◽

Vol 11 (7) ◽

pp. 2139

Author(s):

Feilong Deng ◽

Yushan Li ◽

Yunjuan Peng ◽

Xiaoyuan Wei ◽

Xiaofan Wang ◽

...

Keyword(s):

Relative Abundance ◽

Antibiotic Resistance Genes ◽

Alpha Diversity ◽

Distance Matrix ◽

Archaeal Community ◽

Gene Families ◽

Shannon Index ◽

Metabolic Potential ◽

Substantial Progress ◽

Archaeal Communities

Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray–Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

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Dynamics of Diversity and Abundance of Sulfonamide Resistant Bacteria in a Silt Loam Soil Fertilized by Compost

Antibiotics ◽

10.3390/antibiotics10060699 ◽

2021 ◽

Vol 10 (6) ◽

pp. 699

Author(s):

Hui Han ◽

Mohan Bai ◽

Yanting Chen ◽

Yali Gong ◽

Ming Wu ◽

...

Keyword(s):

High Throughput ◽

Relative Abundance ◽

High Throughput Sequencing ◽

Resistant Bacteria ◽

Arable Soils ◽

Soil Bacterial Communities ◽

Sulfonamide Resistance ◽

Loam Soil ◽

Abundance And Diversity ◽

Sulfonamide Resistance Genes

Although composting is effective in deactivating antibiotic substances in manure, the influence of compost fertilization on the occurrence and dissemination of antibiotic resistance in arable soils remains to be controversial. Herein, the abundance and diversity of two sulfonamide resistance genes (sul1 and sul2) in soil fertilized by compost spiked with two concentrations of sulfadiazine (1 and 10 mg kg−1) were studied intensively by qPCR and high throughput sequencing based on a two-month microcosm experiment. The concentration of sulfadiazine decreased rapidly after spiking from 25% at Day 1 to less than 2.7% at Day 60. Relative abundance of both sul1 and sul2 were significantly higher in soil amended with compost than the non-amended control at Day 1 and slightly decreased with incubation time except for sul2 in the S10 treatment. Soil bacterial communities were transiently shifted by compost fertilization regardless of the presence of sulfadiazine. Relative abundance of genera in three hubs positively interlinked with sul1 and sul2 were significantly higher in compost treated soil than the control at Day 1, 7 and 21, but not at Day 60. High throughput sequencing analyses revealed that most detected (>67% in relative abundance) sul1 and sul2 genotypes sharing >99% similarity with those found in gammaproteobacterial pathogens frequently were commonly present in compost and soil. These results indicated that compost fertilization might increase the abundance rather than diversity of sulfadiazine-resistant populations in soil, which may be facilitated by the presence of sulfadiazine.

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