scholarly journals The Three Domains of Life Within the Discharge Area of a Shallow Subterranean Estuary at a High Energy Beach

2021 ◽  
Vol 9 ◽  
Author(s):  
Julius Degenhardt ◽  
Sahar Khodami ◽  
Felix Milke ◽  
Hannelore Waska ◽  
Bert Engelen ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Sampling Site ◽  
Distribution Patterns ◽  
High Water ◽  
High Energy ◽  
Rrna Gene ◽  
Discharge Area ◽  
Water Line ◽  
Domains Of Life ◽  
Scientific Attention

Subterranean estuaries (STEs) play an important role in linking nutrient cycling between marine and terrestrial systems. As being the primary drivers of nutrient cycling, the composition of microbial communities and their adaptation toward both, terrestrial and marine conditions are of special interest. While bacterial communities of STEs have received increasing scientific attention, archaeal and meiofaunal diversity was mostly neglected. Previous studies at the investigated sampling site, the STE of a mesotidal beach at the German North Sea island of Spiekeroog, focused on spatial and seasonal patterns of geochemical and bacterial diversity. By additionally investigating the archaeal and meiofaunal diversity and distribution, we now aimed to fill this gap of knowledge to understand the microbial response to submarine groundwater discharge (SGD). The topography of Spiekeroog beach and associated geochemical gradients in porewater displayed a distinct cross-shore zonation, with seawater infiltration on the upper beach at the high water line (HWL), and saline and brackish porewater exfiltration (SGD) at the ridge-runnel structure and the low water line (LWL) on the lower beach. This led to a higher evenness of prokaryotic communities in lower beach areas impacted by SGD compared to unimpacted areas. Archaea contributed 1–4% to the 16S rRNA gene sequence dataset. Those were dominated by Nitrosopumilaceae, corresponding well to higher concentrations of NH4+ in the discharge area of the STE. The unimpacted sites had elevated abundances of Wosearchaeia, which were also detected previously in impacted areas of an STE at Mobile Bay (Gulf of Mexico). While a large proportion of prokaryotes were present in the entire intertidal area, meiofaunal community compositions were site specific and dominated by nematodes. Nematode communities of the high-water line differed distinctively from the other sites. Overall, our data indicates that the three domains of life display distinctly different adaptations when facing the same conditions within the STE. Therefore, distribution patterns of any domain can only be understood if all of them, together with basic environmental information are investigated in an integrated context.

scholarly journals Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3)

2017 ◽  
Vol 83 (10) ◽  
Author(s):  
Ibrahim F. Farag ◽  
Noha H. Youssef ◽  
Mostafa S. Elshahed
Keyword(s):  
16S Rrna ◽  
Sampling Site ◽  
Distribution Patterns ◽  
Global Distribution ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Data Sets ◽  
Aquatic Habitats ◽  
Content Type ◽  
Wide Range

ABSTRACT We investigated the global distribution patterns and pangenomic diversity of the candidate phylum “Latescibacteria” (WS3) in 16S rRNA gene as well as metagenomic data sets. We document distinct distribution patterns for various “Latescibacteria” orders in 16S rRNA gene data sets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68.9 Mb of “Latescibacteria”-affiliated contigs in publicly available metagenomic data sets comprising 73,079 proteins. Metabolic reconstruction suggests a prevalent saprophytic lifestyle in all “Latescibacteria” orders, with marked capacities for the degradation of proteins, lipids, and polysaccharides predominant in plant, bacterial, fungal/crustacean, and eukaryotic algal cell walls. As well, extensive transport and central metabolic pathways for the metabolism of imported monomers were identified. Interestingly, genes and domains suggestive of the production of a cellulosome—e.g., protein-coding genes harboring dockerin I domains attached to a glycosyl hydrolase and scaffoldin-encoding genes harboring cohesin I and CBM37 domains—were identified in order PBSIII_9, GN03, and MSB-4E2 fragments recovered from four anoxic aquatic habitats; hence extending the cellulosomal production capabilities in Bacteria beyond the Gram-positive Firmicutes. In addition to fermentative pathways, a complete electron transport chain with terminal cytochrome c oxidases Caa3 (for operation under high oxygen tension) and Cbb3 (for operation under low oxygen tension) were identified in PBSIII_9 and GN03 fragments recovered from oxygenated and partially/seasonally oxygenated aquatic habitats. Our metagenomic recruitment effort hence represents a comprehensive pangenomic view of this yet-uncultured phylum and provides insights broader than and complementary to those gained from genome recovery initiatives focusing on a single or few sampled environments. IMPORTANCE Our understanding of the phylogenetic diversity, metabolic capabilities, and ecological roles of yet-uncultured microorganisms is rapidly expanding. However, recent efforts mainly have been focused on recovering genomes of novel microbial lineages from a specific sampling site, rather than from a wide range of environmental habitats. To comprehensively evaluate the genomic landscape, putative metabolic capabilities, and ecological roles of yet-uncultured candidate phyla, efforts that focus on the recovery of genomic fragments from a wide range of habitats and that adequately sample the intraphylum diversity within a specific target lineage are needed. Here, we investigated the global distribution patterns and pangenomic diversity of the candidate phylum “Latescibacteria.” Our results document the preference of specific “Latescibacteria” orders to specific habitats, the prevalence of plant polysaccharide degradation abilities within all “Latescibacteria” orders, the occurrence of all genes/domains necessary for the production of cellulosomes within three “Latescibacteria” orders (GN03, PBSIII_9, and MSB-4E2) in data sets recovered from anaerobic locations, and the identification of the components of an aerobic respiratory chain, as well as occurrence of multiple O2-dependent metabolic reactions in “Latescibacteria” orders GN03 and PBSIII_9 recovered from oxygenated habitats. The results demonstrate the value of phylocentric pangenomic surveys for understanding the global ecological distribution and panmetabolic abilities of yet-uncultured microbial lineages since they provide broader and more complementary insights than those gained from single-cell genomic and/or metagenomic-enabled genome recovery efforts focusing on a single sampling site.

scholarly journals Collection of a Bacterial Community Reconstructed from Marine Metagenomes Derived from Jinhae Bay, South Korea

Data ◽  
2021 ◽  
Vol 6 (5) ◽  
pp. 44
Author(s):  
Jae-Hyun Lim ◽  
Il-Nam Kim
Keyword(s):  
Microbial Community ◽  
South Korea ◽  
Microbial Communities ◽  
Marine Bacteria ◽  
Sampling Site ◽  
Community Change ◽  
Rrna Gene ◽  
Water Column Stratification ◽  
Metagenomics Data ◽  
Jinhae Bay

Marine bacteria are known to play significant roles in marine biogeochemical cycles regarding the decomposition of organic matter. Despite the increasing attention paid to the study of marine bacteria, research has been too limited to fully elucidate the complex interaction between marine bacterial communities and environmental variables. Jinhae Bay, the study area in this work, is the most anthropogenically eutrophied coastal bay in South Korea, and while its physical and biogeochemical characteristics are well described, less is known about the associated changes in microbial communities. In the present study, we reconstructed a metagenomics data based on the 16S rRNA gene to investigate temporal and vertical changes in microbial communities at three depths (surface, middle, and bottom) during a seven-month period from June to December 2016 at one sampling site (J1) in Jinhae Bay. Of all the bacterial data, Proteobacteria, Bacteroidetes, and Cyanobacteria were predominant from June to November, whereas Firmicutes were predominant in December, especially at the middle and bottom depths. These results show that the composition of the microbial community is strongly associated with temporal changes. Furthermore, the community compositions were markedly different between the surface, middle, and bottom depths in summer, when water column stratification and bottom water hypoxia (low dissolved oxygen level) were strongly developed. Metagenomics data contribute to improving our understanding of important relationships between environmental characteristics and microbial community change in eutrophication-induced and deoxygenated coastal areas.

scholarly journals Macrozoobenthos in an altitudinal gradient in North Patagonian Cautín River (Araucanía Region, Chile)

2022 ◽  
Vol 82 ◽  
Author(s):  
D. Figueroa ◽  
P. De los Rios-Escalante
Keyword(s):  
Water Quality ◽  
Sampling Site ◽  
Benthic Fauna ◽  
Distribution Patterns ◽  
Macroinvertebrate Communities ◽  
Cultural Activity ◽  
Dissolved Oxygen Concentration ◽  
Dominant Group ◽  
Altitudinal Distribution ◽  
Water Quality Indicators

Abstract The Cautín River is closely related with the economic development of Temuco city, (38°S; Chile). Existing knowledge of the Cautín River is limited to information about its biological characteristics as a reference for the evaluation and assessment of water quality. The object of this study was to develop taxonomic characterisation of the benthic macroinvertebrates along the main course of the Cautín River, and to study the community structure using correlation analysis between community parameters. To carry out this research, the macroinvertebrate community was studied in 10 sampling sites distributed along the main course of the river. The samples were taken in summer (1997 and 2000), when optimal hydrological conditions existed. Analysis of the samples showed that the benthic fauna was composed of 56 taxa, the dominant group being insects with 48 taxa. Three main sectors were recognised in the course of the Cautín River: high, middle and low. Each sector has restricted-distribution species, while other species are widely distributed along the river. These distribution patterns seem to be influenced by dissolved oxygen concentration, temperature, altitudinal distribution and anthropo-cultural activity, present at every sampling site. Finally, this research provides a first approach to the biology of the Cautín River. Further studies could be planned on the basis of this knowledge to investigate water quality indicators based on macroinvertebrate communities.

scholarly journals Influence of Sampling Site and other Environmental Factors on the Bacterial Community Composition of Domestic Washing Machines

2019 ◽  
Vol 8 (1) ◽  
pp. 30 ◽  
Author(s):  
Susanne Jacksch ◽  
Dominik Kaiser ◽  
Severin Weis ◽  
Mirko Weide ◽  
Stefan Ratering ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Community Composition ◽  
Sampling Site ◽  
Alpha Diversity ◽  
Growth Conditions ◽  
Microbial Colonization ◽  
Rrna Gene ◽  
Washing Machines ◽  
16S Rrna Gene Pyrosequencing ◽  
Machine Parts

Modern, mainly sustainability-driven trends, such as low-temperature washing or bleach-free liquid detergents, facilitate microbial survival of the laundry processes. Favourable growth conditions like humidity, warmth and sufficient nutrients also contribute to microbial colonization of washing machines. Such colonization might lead to negatively perceived staining, corrosion of washing machine parts and surfaces, as well as machine and laundry malodour. In this study, we characterized the bacterial community of 13 domestic washing machines at four different sampling sites (detergent drawer, door seal, sump and fibres collected from the washing solution) using 16S rRNA gene pyrosequencing and statistically analysed associations with environmental and user-dependent factors. Across 50 investigated samples, the bacterial community turned out to be significantly site-dependent with the highest alpha diversity found inside the detergent drawer, followed by sump, textile fibres isolated from the washing solution, and door seal. Surprisingly, out of all other investigated factors only the monthly number of wash cycles at temperatures ≥ 60 °C showed a significant influence on the community structure. A higher number of hot wash cycles per month increased microbial diversity, especially inside the detergent drawer. Potential reasons and the hygienic relevance of this finding need to be assessed in future studies.

scholarly journals Microscopic Determination of Remaining Oil Distribution in Sandstones With Different Permeability Scales Using Computed Tomography Scanning

2019 ◽  
Vol 141 (9) ◽  
Author(s):  
Yongfei Yang ◽  
Haiyuan Yang ◽  
Liu Tao ◽  
Jun Yao ◽  
Wendong Wang ◽  
...  
Keyword(s):  
Distribution Pattern ◽  
Oil Recovery ◽  
Distribution Patterns ◽  
High Water ◽  
Water Flooding ◽  
Oil Distribution ◽  
Computed Tomography Scanning ◽  
Remaining Oil ◽  
High Water Cut ◽  
Water Cut

To investigate the characteristics of oil distribution in porous media systems during a high water cut stage, sandstones with different permeability scales of 53.63 × 10−3 μm2 and 108.11 × 10−3 μm2 were imaged under a resolution of 4.12 μm during a water flooding process using X-ray tomography. Based on the cluster-size distribution of oil segmented from the tomography images and through classification using the shape factor and Euler number, the transformation of the oil distribution pattern in different injection stages was studied for samples with different pore structures. In general, the distribution patterns of an oil cluster continuously change during water injection. Large connected oil clusters break off into smaller segments. The sandstone with a higher permeability (108.11 × 10−3 μm2) shows the larger change in distribution pattern, and the remaining oil is trapped in the pores with a radius of approximately 7–12 μm. Meanwhile, some disconnected clusters merge together and lead to a re-connection during the high water cut period. However, the pore structure becomes compact and complex, the residual nonwetting phase becomes static and is difficult to move; and thus, all distribution patterns coexist during the entire displacement process and mainly distribute in pores with a radius of 8–12 μm. For the pore-scale entrapment characteristics of the oil phase during a high water cut period, different enhance oil recovery (EOR) methods should be considered in sandstones correspondent to each permeability scale.

scholarly journals Alterations in Rumen Bacterial Community and Metabolome Characteristics of Cashmere Goats in Response to Dietary Nutrient Density

Animals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1193
Author(s):  
Yaoyue Wang ◽  
Peng Tang ◽  
Yafei Xiao ◽  
Jianming Liu ◽  
Yulin Chen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Metabolic Pathways ◽  
High Energy ◽  
High Protein ◽  
Metabolic Energy ◽  
Control Group ◽  
Rrna Gene ◽  
Dietary Energy ◽  
Nutrient Density ◽  
Cashmere Goats

This study was conducted to investigate the impacts of dietary energy and protein on rumen bacterial composition and ruminal metabolites. A total of 12 ruminal samples were collected from Shaanbei white cashmere goats which were divided into two groups, including high-energy and high-protein (Group H; crude protein, CP: 9.37% in dry matter; metabolic energy, ME: 9.24 MJ/kg) and control (Group C; CP: 8.73%; ME: 8.60 MJ/kg) groups. Thereby, 16S rRNA gene sequencing and a quantitative polymerase chain reaction were performed to identify the rumen bacterial community. Metabolomics analysis was done to investigate the rumen metabolites and the related metabolic pathways in Groups C and H. The high-energy and high-protein diets increased the relative abundance of phylum Bacteroidetes and genera Prevotella_1 and Succiniclasticum, while decreasing the number of Proteobacteria (p < 0.05). The dominant differential metabolites were amino acids, peptides, and analogs. Tyrosine metabolism played an important role among the nine main metabolic pathways. Correlation analysis revealed that both Prevotella_1 (r = 0.608, p < 0.05) and Ruminococcus_2 (r = 0.613, p < 0.05) showed a positive correlation with catechol. Our findings revealed that the diets with high energy and protein levels in Group H significantly altered the composition of ruminal bacteria and metabolites, which can help to improve the dietary energy and protein use efficiency in goats.

scholarly journals phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Harald R. Gruber-Vodicka ◽  
Brandon K. B. Seah ◽  
Elmar Pruesse
Keyword(s):  
High Throughput ◽  
Small Subunit ◽  
General Purpose ◽  
Reference Database ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Ssu Rrna Gene ◽  
Domains Of Life ◽  
Environmental Microbes

ABSTRACT The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual. IMPORTANCE To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing.

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