scholarly journals Bacterial and Archaeal Communities in Polymetallic Nodules, Sediments, and Bottom Waters of the Abyssal Clarion-Clipperton Zone: Emerging Patterns and Future Monitoring Considerations

2021 ◽  
Vol 8 ◽  
Author(s):  
Emma K. Wear ◽  
Matthew J. Church ◽  
Beth N. Orcutt ◽  
Christine N. Shulse ◽  
Markus V. Lindh ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Deep Sea ◽  
North Pacific Ocean ◽  
Regional Scale ◽  
Future Research ◽  
Rrna Gene ◽  
Biogeographic Patterns ◽  
Bacterial And Archaeal Communities ◽  
Relative Abundances ◽  
Archaeal Communities

Bacteria and archaea are key contributors to deep-sea biogeochemical cycles and food webs. The disruptions these microbial communities may experience during and following polymetallic nodule mining in the Clarion-Clipperton Zone (CCZ) of the North Pacific Ocean could therefore have broad ecological effects. Our goals in this synthesis are to characterize the current understanding of biodiversity and biogeography of bacteria and archaea in the CCZ and to identify gaps in the baseline data and sampling approaches, prior to the onset of mining in the region. This is part of a large effort to compile biogeographic patterns in the CCZ, and to assess the representivity of no-mining Areas of Particular Environmental Interest, across a range of taxa. Here, we review published studies and an additional new dataset focused on 16S ribosomal RNA (rRNA) gene amplicon characterization of abyssal bacterial and archaeal communities, particularly focused on spatial patterns. Deep-sea habitats (nodules, sediments, and bottom seawater) each hosted significantly different microbial communities. An east-vs.-west CCZ regional distinction was present in nodule communities, although the magnitude was small and likely not detectable without a high-resolution analysis. Within habitats, spatial variability was driven by differences in relative abundances of taxa, rather than by abundant taxon turnover. Our results further support observations that nodules in the CCZ have distinct archaeal communities from those in more productive surrounding regions, with higher relative abundances of presumed chemolithoautotrophic Nitrosopumilaceae suggesting possible trophic effects of nodule removal. Collectively, these results indicate that bacteria and archaea in the CCZ display previously undetected, subtle, regional-scale biogeography. However, the currently available microbial community surveys are spatially limited and suffer from sampling and analytical differences that frequently confound inter-comparison; making definitive management decisions from such a limited dataset could be problematic. We suggest a number of future research priorities and sampling recommendations that may help to alleviate dataset incompatibilities and to address challenges posed by rapidly advancing DNA sequencing technology for monitoring bacterial and archaeal biodiversity in the CCZ. Most critically, we advocate for selection of a standardized 16S rRNA gene amplification approach for use in the anticipated large-scale, contractor-driven biodiversity monitoring in the region.

scholarly journals Soil Depth Determines the Composition and Diversity of Bacterial and Archaeal Communities in a Poplar Plantation

Forests ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 550 ◽  
Author(s):  
Huili Feng ◽  
Jiahuan Guo ◽  
Weifeng Wang ◽  
Xinzhang Song ◽  
Shuiqiang Yu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Rrna Gene ◽  
Poplar Plantation ◽  
Plantation Forest ◽  
Bacterial And Archaeal Communities ◽  
Different Depths ◽  
Archaeal Communities

Understanding the composition and diversity of soil microorganisms that typically mediate the soil biogeochemical cycle is crucial for estimating greenhouse gas flux and mitigating global changes in plantation forests. Therefore, the objectives of this study were to investigate changes in diversity and relative abundance of bacteria and archaea with soil profiles and the potential factors influencing the vertical differentiation of microbial communities in a poplar plantation. We investigated soil bacterial and archaeal community compositions and diversities by 16S rRNA gene Illumina MiSeq sequencing at different depths of a poplar plantation forest in Chenwei forest farm, Sihong County, Jiangsu, China. More than 882,422 quality-filtered 16S rRNA gene sequences were obtained from 15 samples, corresponding to 34 classified phyla and 68 known classes. Ten major bacterial phyla and two archaeal phyla were found. The diversity of bacterial and archaeal communities decreased with depth of the plantation soil. Analysis of variance (ANOVA) of relative abundance of microbial communities exhibited that Nitrospirae, Verrucomicrobia, Latescibacteria, GAL15, SBR1093, and Euryarchaeota had significant differences at different depths. The transition zone of the community composition between the surface and subsurface occurred at 10–20 cm. Overall, our findings highlighted the importance of depth with regard to the complexity and diversity of microbial community composition in plantation forest soils.

scholarly journals Development of chemosynthetic microbial communities in organic falls deployed in the deep Southwest Atlantic Ocean

2021 ◽  
Author(s):  
Augusto M. Amendola ◽  
Francielli V. Peres ◽  
Julio C. F. Moreira ◽  
Paulo Y. G. Sumida ◽  
Fabiana S. Paula ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Deep Sea ◽  
Organic Substrates ◽  
Southwest Atlantic ◽  
Factors Affecting ◽  
The North ◽  
Significant Difference ◽  
Bacterial And Archaeal Communities ◽  
Fall Experiment ◽  
Archaeal Communities

ABSTRACTThe assembly and successional processes of microbial communities inhabiting deep-sea whale and wood falls are highly complex and vastly unknown, as a myriad of factors may affect the development of a chemosynthetic-based ecosystem on these organic islands. The chemoautotrophy supported by organic substrates is the basis of long-lasting ecosystems, considered biodiversity hotspots in the oligotrophic deep sea. Understanding how these microbial communities develop and the factors affecting them could shed light on processes related to the maintenance of biodiversity in this environment. We performed a whale- and wood-fall experiment in the southwest Atlantic on the Brazilian continental margin and investigated biofilm-forming bacterial and archaeal communities colonising these substrates, deployed at 1500 and 3300 m depth. The composition of the prokaryotic communities shared some similarities with previously reported organic falls in the north Pacific and the Mediterranean Sea, mainly regarding sulphur oxidising chemolithotrophic taxa from the phyla Campylobacterota and Proteobacteria. Communities were found to be highly different between the organic substrates, as whale fall associated biofilms presented a higher dominance of sulphur oxidising chemolithotrophs. We also observed a significant difference between the two sites, with the whale associated communities at the 1500 isobath presenting a faster establishment of the chemosynthetic taxa.

scholarly journals Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters

2020 ◽  
Vol 8 (2) ◽  
pp. 198
Author(s):  
Mingyue Li ◽  
Tiezhu Mi ◽  
Zhigang Yu ◽  
Manman Ma ◽  
Yu Zhen
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Archaeal Community ◽  
Rrna Gene ◽  
Liaohe River ◽  
Estuarine Wetland ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO4-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.

scholarly journals Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Tess E. Brewer ◽  
Emma L. Aronson ◽  
Keshav Arogyaswamy ◽  
Sharon A. Billings ◽  
Jon K. Botthoff ◽  
...  
Keyword(s):  
United States ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
The United States ◽  
Soil Profiles ◽  
Growth Strategies ◽  
Surface Soils ◽  
Wide Range ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

ABSTRACT While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments. IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

scholarly journals Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene

2019 ◽  
Author(s):  
Wenjing Qiao ◽  
Luz A. Puentes Jácome ◽  
Xianjin Tang ◽  
Line Lomheim ◽  
Minqing Ivy Yang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Contaminated Sites ◽  
Molar Ratio ◽  
Rrna Gene ◽  
Absolute Abundance ◽  
Hch Isomers ◽  
Persistent Pesticide ◽  
Hexachlorocyclohexane Isomers ◽  
Archaeal Communities

AbstractIntensive historical and worldwide use of the persistent pesticide technical-grade hexachlorocyclohexane (HCH), composed of the active ingredient γ-HCH (called lindane) along with several other HCH isomers, has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of α-, β-, γ-, and δ-HCH isomers stoichiometrically and completely to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates increased progressively from <3 µM/day to ∼12 µM/day over two years. The molar ratio of benzene to MCB produced was a function of the substrate isomer, and ranged from β (0.77±0.15), α (0.55±0.09), γ (0.13±0.02) to δ (0.06±0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundance of Pelobacter and Dehalobacter, especially in the α-HCH and δ-HCH cultures. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of α-, β-, γ-, and δ-HCH, a key step towards better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.

scholarly journals Estimation of microbial metabolism and co-occurrence patterns in fracture groundwaters of deep crystalline bedrock at Olkiluoto, Finland

2015 ◽  
Vol 12 (16) ◽  
pp. 13819-13857 ◽  
Author(s):  
M. Bomberg ◽  
T. Lamminmäki ◽  
M. Itävaara
Keyword(s):  
Microbial Communities ◽  
Physicochemical Parameters ◽  
Calvin Cycle ◽  
Acid Oxidation ◽  
Core Microbiome ◽  
Rare Taxa ◽  
The Core ◽  
Crystalline Bedrock ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

Abstract. The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is great but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. The great sequencing depth revealed that up to 95 and 99 % of the bacterial and archaeal communities, respectively, were composed of only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3 and 6 fold more bacterial and archaeal taxa. Several clusters of co-occurring rare taxa were identified, which correlated significantly with physicochemical parameters, such as salinity, concentration of inorganic or organic carbon, sulphur, pH and depth. The metabolic properties of the microbial communities were predicted using PICRUSt. The rough prediction showed that the metabolic pathways included commonly fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier conditions on Earth, but could also be induced again if changes in their living conditions occur. In this study only the rare taxa correlated with any physicochemical parameters. Thus these microorganisms can respond to environmental change caused by physical or biological factors that may lead to alterations in the diversity and function of the microbial communities in crystalline bedrock environments.

scholarly journals Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons

2019 ◽  
Author(s):  
Tess E. Brewer ◽  
Emma L. Aronson ◽  
Keshav Arogyaswamy ◽  
Sharon A. Billings ◽  
Jon K. Botthoff ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Depth ◽  
Soil Microbial Communities ◽  
Soil Profiles ◽  
Growth Strategies ◽  
Surface Soils ◽  
Wide Range ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities ◽  
The U.S

AbstractWhile most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the U.S. to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.ImportanceSoil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the U.S., we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored distinct communities compared to the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising amount of novel microbes with unique adaptations to oligotrophic subsurface conditions.

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