scholarly journals The Saltpan Microbiome Is Structured by Sediment Depth and Minimally Influenced by Variable Hydration

2020 ◽  
Vol 8 (4) ◽  
pp. 538
Author(s):  
Eric A. Weingarten ◽  
Lauren A. Lawson ◽  
Colin R. Jackson
Keyword(s):  
Surface Sediment ◽  
Gulf Coast ◽  
Archaeal Community ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Marine Microorganisms ◽  
Sediment Depth ◽  
Ephemeral Wetland ◽  
Brackish Marshes ◽  
Mississippi Gulf Coast

Saltpans are a class of ephemeral wetland characterized by alternating periods of inundation, rising salinity, and desiccation. We obtained soil cores from a saltpan on the Mississippi Gulf coast in both the inundated and desiccated state. The microbiomes of surface and 30 cm deep sediment were determined using Illumina sequencing of the V4 region of the 16S rRNA gene. Bacterial and archaeal community composition differed significantly between sediment depths but did not differ between inundated and desiccated states. Well-represented taxa included marine microorganisms as well as multiple halophiles, both observed in greater proportions in surface sediment. Functional inference of metagenomic data showed that saltpan sediments in the inundated state had greater potential for microbial activity and that several energetic and degradation pathways were more prevalent in saltpan sediment than in nearby tidal marsh sediment. Microbial communities within saltpan sediments differed in composition from those in adjacent freshwater and brackish marshes. These findings indicate that the bacterial and archaeal microbiomes of saltpans are highly stratified by sediment depth and are only minimally influenced by changes in hydration. The surface sediment community is likely isolated from the shallow subsurface community by compaction, with the microbial community dominated by marine and terrestrial halophiles.

scholarly journals Bioinformatic approaches for analysis of coral-associated bacteria using R programming language

2021 ◽  
Vol 18 (4) ◽  
pp. 733-743
Author(s):  
Doan Thi Nhung ◽  
Bui Van Ngoc
Keyword(s):  
Programming Language ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Marine Microorganisms ◽  
Taxonomic Assignment ◽  
Associated Bacteria ◽  
R Programming Language ◽  
R Programming

Recent advances in metagenomics and bioinformatics allow the robust analysis of the composition and abundance of microbial communities, functional genes, and their metabolic pathways. So far, there has been a variety of computational/statistical tools or software for analyzing microbiome, the common problems that occurred in its implementation are, however, the lack of synchronization and compatibility of output/input data formats between such software. To overcome these challenges, in this study context, we aim to apply the DADA2 pipeline (written in R programming language) instead of using a set of different bioinformatics tools to create our own workflow for microbial community analysis in a continuous and synchronous manner. For the first effort, we tried to investigate the composition and abundance of coral-associated bacteria using their 16S rRNA gene amplicon sequences. The workflow or framework includes the following steps: data processing, sequence clustering, taxonomic assignment, and data visualization. Moreover, we also like to catch readers’ attention to the information about bacterial communities living in the ocean as most marine microorganisms are unculturable, especially residing in coral reefs, namely, bacteria are associated with the coral Acropora tenuis in this case. The outcomes obtained in this study suggest that the DADA2 pipeline written in R programming language is one of the potential bioinformatics approaches in the context of microbiome analysis other than using various software. Besides, our modifications for the workflow execution help researchers to illustrate metagenomic data more easily and systematically, elucidate the composition, abundance, diversity, and relationship between microorganism communities as well as to develop other bioinformatic tools more effectively.

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.

scholarly journals From Disaster to Resilience

2015 ◽  
Author(s):  
David Perkes ◽  
Keyword(s):  
Hurricane Katrina ◽  
Disaster Response ◽  
Gulf Coast ◽  
Community Design ◽  
Design Studio ◽  
Mississippi State University ◽  
State University ◽  
Art And Design ◽  
Mississippi Gulf Coast

What is changing in the world so that the word “resilience” is so frequently used? 2015 marks the ten year anniversary of Hurricane Katrina and the five year anniversary of the Gulf of Mexico oil spill. The Gulf Coast Community Design Studio has been working on the Mississippi Gulf Coast since Hurricane Katrina and their work provides the vantage point of this paper. The Gulf Coast Community Design Studio is an off-campus research and service center of Mississippi State University College of Architecture, Art and Design located in Biloxi, Mississippi. It was created to respond to Hurricane Katrina and has evolved from disaster response to long-term efforts of resilience. The design studio’s evolution is not an isolated story. It is part of a national move toward resilience.

Status, Distribution, and Habitat Use of Coastal Waterbirds along the Mississippi Gulf Coast, USA

Waterbirds ◽  
2021 ◽  
Vol 44 (2) ◽  
Author(s):  
Abigail J. Darrah ◽  
Timothy D. Meehan ◽  
Nicole L. Michel
Keyword(s):  
Habitat Use ◽  
Gulf Coast ◽  
Mississippi Gulf Coast

Nitrogen cycling in Louisiana Gulf Coast brackish marshes

Hydrobiologia ◽  
1990 ◽  
Vol 199 (1) ◽  
pp. 73-79 ◽  
Author(s):  
R. D. DeLaune ◽  
W. H. Patrick
Keyword(s):  
Nitrogen Cycling ◽  
Gulf Coast ◽  
Brackish Marshes

scholarly journals Lutibacter citreus sp. nov., isolated from Arctic surface sediment

2020 ◽  
Vol 70 (5) ◽  
pp. 3154-3161 ◽  
Author(s):  
Zhao-Zhong Du ◽  
Liu-Yan Zhou ◽  
Tao-Jie Wang ◽  
Hui-Rong Li ◽  
Zong-Jun Du
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Surface Sediment ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
The Arctic ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, aerobic, non-motile, non-gliding, yellow-pigmented and rod-shaped bacterial strain, designated 1KV19T, was isolated from a surface sediment sample collected near a bay in the Arctic. Growth of strain 1KV19T occurred in 1–4 % (w/v) NaCl (optimum, 2 %), at 4–35 °C (optimum, 25–30 °C) and at pH 6.5–8.0 (optimum, pH 7.0–7.5). The phylogenetic trees based on the 16S rRNA gene sequences showed that strain 1KV19T was associated with the genus Lutibacter and had the highest 16S rRNA gene sequence similarity to Lutibacter oceani 325-5T with 98.1 % similarity. Similarity values between strain 1KV19T and the type strains of other Lutibacter species were in the range 95.9–97.6 %. The average nucleotide identity and digital DNA–DNA hybridization values between strain 1KV19T and related species of the genus Lutibacter were 76.4–79.1 and 19.9–22.3 %, respectively. The major cellular fatty acids of strain 1KV19T were iso-C15 : 0 3-OH, iso-C15 : 0 and iso-C16 : 1 H. The respiratory quinone was MK-6. The major polar lipids of strain 1KV19T were phosphatidylethanolamine, one unidentified aminolipid and two unidentified polar lipids. The phenotypic, genotypic and chemotaxonomic differences between strain 1KV19T and its phylogenetic relatives indicate that strain 1KV19T should be regarded as representing a novel species in the genus Lutibacter , for which the name Lutibacter citreus sp. nov. is proposed. The type strain is 1KV19T (=KCTC 62595T=MCCC 1H00307T).

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.

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