scholarly journals Metagenomic insights into ecosystem function in the microbial mats of Blue Holes, Shark Bay

2020 ◽  
Author(s):  
Gareth S Kindler ◽  
Hon Lun Wong ◽  
Anthony W D Larkum ◽  
Michael Johnson ◽  
Fraser I MacLeod ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Diversity Indices ◽  
Microbial Interactions ◽  
Adaptive Responses ◽  
Shark Bay ◽  
Diverse Community ◽  
Assimilatory Sulfate Reduction ◽  
Blue Holes

AbstractMicrobial mat ecosystems vary in complexity and structure depending on the environmental constraints placed by nature. Here, we describe in detail for the first time the community composition and functional potential of the microbial mats found in the supratidal, gypsum-rich, and hypersaline region of Blue Holes, Shark Bay. This was achieved via high throughput sequencing of total mat community DNA on the Illumina NextSeq platform. Mat communities were mainly comprised of Proteobacteria (29%), followed by Bacteroidetes/Chlorobi Group (11%), and Planctomycetes (10%). These mats were found to also harbor a diverse community of potentially novel microorganisms including members from the DPANN and Asgard archaea, Candidate Phyla Radiation (CPR) and other candidate phyla, with highest diversity indices found in the lower regions of the mat. Major metabolic cycles belonging to sulfur, carbon, nitrogen, and fermentation were detected in the mat metagenomes with the assimilatory sulfate reduction pathway being distinctly abundant. Critical microbial interactions were also inferred, and from 117 medium-to-high quality metagenome-assembled genomes (MAGs), viral defense mechanisms (CRISPR, BREX, and DISARM), elemental transport, osmoprotection, heavy metal and UV resistance were also detected in the mats. These analyses have provided a greater understanding of these distinct mat systems in Shark Bay, including key insights into adaptive responses.

scholarly journals Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses

2020 ◽  
Vol 11 ◽  
Author(s):  
Matthew A. Campbell ◽  
Kliti Grice ◽  
Pieter T. Visscher ◽  
Therese Morris ◽  
Hon Lun Wong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microbial Mats ◽  
Functional Gene ◽  
Adaptive Responses ◽  
Shark Bay ◽  
Hypersaline Microbial Mats

scholarly journals Increasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics

2021 ◽  
Vol 9 (2) ◽  
pp. 249
Author(s):  
Thomas Schalck ◽  
Bram Van den Bergh ◽  
Jan Michiels
Keyword(s):  
Stress Responses ◽  
Small Rnas ◽  
Defense Mechanisms ◽  
Industrial Processes ◽  
Solvent Tolerance ◽  
Adaptive Responses ◽  
Environment Friendly ◽  
Pathway Optimization ◽  
Polymer Precursors ◽  
Product Accumulation

Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.

scholarly journals The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 745
Author(s):  
Michelle Martin de Bustamante ◽  
Diego Gomez ◽  
Jennifer MacNicol ◽  
Ralph Hamor ◽  
Caryn Plummer
Keyword(s):  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Bacterial Microbiota ◽  
Healthy Control ◽  
Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

scholarly journals The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer?

2011 ◽  
Vol 301 (3) ◽  
pp. G401-G424 ◽  
Author(s):  
M. Andrea Azcárate-Peril ◽  
Michael Sikes ◽  
José M. Bruno-Bárcena
Keyword(s):  
Colorectal Cancer ◽  
Intestinal Microbiota ◽  
Defense Mechanisms ◽  
High Throughput Sequencing ◽  
Safety Evaluation ◽  
Health Benefit ◽  
The United States ◽  
Dietary Factors ◽  
Colorectal Adenomas ◽  
Food Allergies

Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the United States, and, even though 5–15% of the total CRC cases can be attributed to individual genetic predisposition, environmental factors could be considered major factors in susceptibility to CRC. Lifestyle factors increasing the risks of CRC include elevated body mass index, obesity, and reduced physical activity. Additionally, a number of dietary elements have been associated with higher or lower incidence of CRC. In this context, it has been suggested that diets high in fruit and low in meat might have a protective effect, reducing the incidence of colorectal adenomas by modulating the composition of the normal nonpathogenic commensal microbiota. In addition, it has been demonstrated that changes in abundance of taxonomic groups have a profound impact on the gastrointestinal physiology, and an increasing number of studies are proposing that the microbiota mediates the generation of dietary factors triggering colon cancer. High-throughput sequencing and molecular taxonomic technologies are rapidly filling the knowledge gaps left by conventional microbiology techniques to obtain a comprehensive catalog of the human intestinal microbiota and their associated metabolic repertoire. The information provided by these studies will be essential to identify agents capable of modulating the massive amount of gut bacteria in safe noninvasive manners to prevent CRC. Probiotics, defined as “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host” ( 219 ), are capable of transient modulation of the microbiota, and their beneficial effects include reinforcement of the natural defense mechanisms and protection against gastrointestinal disorders. Probiotics have been successfully used to manage infant diarrhea, food allergies, and inflammatory bowel disease; hence, the purpose of this review was to examine probiotic metabolic activities that may have an effect on the prevention of CRC by scavenging toxic compounds or preventing their generation in situ. Additionally, a brief consideration is given to safety evaluation and production methods in the context of probiotics efficacy.

Secretory Proteases of the Human Skin Microbiome

2021 ◽  
Author(s):  
Wisely Chua ◽  
Si En Poh ◽  
Hao Li
Keyword(s):  
Human Skin ◽  
Hydrolytic Enzymes ◽  
Microbial Interactions ◽  
Skin Microbiome ◽  
Protein Cleavage ◽  
Wide Range ◽  
Range Of Functions ◽  
Diverse Community ◽  
Secreted Proteases ◽  
Pathogenic Agents

The human skin is our outermost layer and serves as a protective barrier against external insults. Advances in next generation sequencing have enabled the discoveries of a rich and diverse community of microbes - bacteria, fungi and viruses that are residents of this surface. The genomes of these microbes also revealed the presence of many secretory enzymes. In particular, proteases which are hydrolytic enzymes capable of protein cleavage and degradation are of special interest in the skin environment which is enriched in proteins and lipids. In this minireview, we will focus on the roles of these skin-relevant microbial secreted proteases, both in terms of their widely studied roles as pathogenic agents in tissue invasion and host immune inactivation, and their recently discovered roles in inter-microbial interactions and modulation of virulence factors. From these studies, it has become apparent that while microbial proteases are capable of a wide range of functions, their expression is tightly regulated and highly responsive to the environments the microbes are in. With the introduction of new biochemical and bioinformatics tools to study protease functions, it will be important to understand the roles played by skin microbial secretory proteases in cutaneous health, especially the less studied commensal microbes with an emphasis on contextual relevance.

scholarly journals Microbial colonization of chasmoendolithic habitats in the hyper-arid zone of the Atacama Desert

2012 ◽  
Vol 9 (11) ◽  
pp. 15603-15632
Author(s):  
J. DiRuggiero ◽  
J. Wierzchos ◽  
C. K. Robinson ◽  
T. Souterre ◽  
J. Ravel ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Heterotrophic Bacteria ◽  
Arid Zone ◽  
Atacama Desert ◽  
Community Diversity ◽  
Microbial Colonization ◽  
Climate Data ◽  
Microbial Life ◽  
Total Community ◽  
Diverse Community

Abstract. Efforts in searching for microbial life in the driest part of Atacama Desert, Chile, revealed a small number of lithic habitats that can be considered as environmental refuges for life. In this study, we describe for the first time chasmoendolithic colonization of fissures and cracks of rhyolite-gypsum and calcite rocks collected in the hyper-arid zone of the desert. The use of high-throughput sequencing revealed that the Atacama rock communities comprised a few dominant phylotypes and a number of less abundant taxa representing the majority of the total community diversity. The chasmoendolithic communities were dominated by Chroococcidiopsis species cyanobacteria and supported a number of novel heterotrophic bacteria. Micro-climate data and geomorphic analysis of the mineral substrates suggested higher water availability in the calcite rocks in the form of enhanced water retention in the complex network of cracks and fissures of these rocks as well as increased occurrence of liquid water in the form of dewfall. These characteristics were associated with a diverse community of phototrophic and heterotrophic bacteria in the calcite chasmoendolithic ecosystem. This study is another example of the diversity of adaptive strategies at the limit for life and illustrates that rock colonization is controlled by a complex set of factors.

scholarly journals Ecological status and diversity indices of Panchaule (Dactylorhiza hatagirea) and its associates in Lete village of Mustang district, Nepal

2016 ◽  
Vol 26 (1) ◽  
pp. 45-52 ◽  
Author(s):  
C. B. Khadka ◽  
A. L. Hammet ◽  
A. Singh ◽  
M. K. Balla ◽  
Y. P. Timilsina
Keyword(s):  
Monsoon Season ◽  
Ecological Status ◽  
Diversity Indices ◽  
Ecological Value ◽  
Conservation Area ◽  
Illegal Harvesting ◽  
Diverse Community ◽  
June July ◽  
Important Value Index ◽  
Rheum Australe

This paper focuses on the ecological status and diversity indices: Simson’s Index (C), Simson’s Index of Dominance (D) and Shannon-Weaver Index (H) of Dactylorhiza hatagirea and its associates- Rheum australe and Rumex nepalensis in Lete village of Mustang District within the Annapurna Conservation Area. The study was conducted during the monsoon season (June/July) of 2013 in the Lete VDC of Mustang District. The study site possessed an area of 4.5 ha. Altogether, 100 circular plots, each with 25 m2 area, were laid out purposively within the study area; the sampling intensity being 5.55%. The relative frequency, the relative density, the abundance, the relative coverage and the Important Value Index of the species were found to be 61.11, 53.91, 1,061.54, 72.2 and 187.24 respectively. Similarly, the Simson’s Index (C), the Simson’s Index of Dominance (D) and the Shannon-Weaver Index of the species were found to be 0.41, 0.59 and 3.27 respectively, indicating relatively even and relatively diverse community. The study showed relatively higher values of all the parameters of D. hatagirea as compared to its associates indicating good ecological value. However, threats remain due to the illegal harvesting of this valuable orchid and overgrazing in the study site.Banko JanakariA Journal of Forestry Information for NepalVol. 26, No. 1, Page: 45-52, 2016

Characterization of microbial community in cold-chain hairtail fish by high-throughput sequencing technology

2021 ◽  
Author(s):  
Jiali Xing ◽  
Xiaorong Xu ◽  
Xiaohu Luo ◽  
Ruihang Zheng ◽  
Lingyan Mao ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Flora ◽  
Diversity Indices ◽  
Cold Chain ◽  
Class Level ◽  
The Family ◽  
Dominant Bacteria

Abstract: High-throughput sequencing was used to analyze the microbial communities in the muscle samples of hairtail fish to study their diversity and dynamic changes during cold-chain circulation. The results showed that the richness and diversity of the microbial community in hairtail fish had a transient decline in 0–24 h and decreased after the first rise during 24–216 h. The diversity and richness of bacteria in cold-chain hairtail fish reached the maximum at 168 h. The Shannon and Simpson diversity indices of the bacteria were 2.96 and 0.16, respectively, and their ACE and Chao1 richness indices were 254.84 and 155.10, respectively. In addition, the dominant bacteria were Proteobacteria in the phylum level, Gammaproteobacteria in the class level, Pseudomonadales in the order level, Pseudomonadaceae in the family level, and Pseudomonas in the genus level, and their relative abundance were 80.52%, 72.11%, 76.68%, 23.25%, and 53.50%, respectively. In this study, the structure of bacterial flora and the dominant bacteria in cold-chain hairtail fish were analyzed by high-throughput sequencing to provide a basis for exploring how to maintain the freshness of hairtail fish and for predicting the shelf-life of hairtail fish.

scholarly journals DNA metabarcoding of fungal diversity in air and snow of Livingston Island, South Shetland Islands, Antarctica

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Luiz Henrique Rosa ◽  
Otávio Henrique Bezerra Pinto ◽  
Tina Šantl-Temkiv ◽  
Peter Convey ◽  
Micheline Carvalho-Silva ◽  
...  
Keyword(s):  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Rank Order ◽  
Mesh Size ◽  
Diversity Indices ◽  
South Shetland Islands ◽  
Livingston Island ◽  
Dna Metabarcoding ◽  
Air Sample ◽  
Total Dna

AbstractWe assessed fungal diversity present in air and freshly deposited snow samples obtained from Livingston Island, Antarctica, using DNA metabarcoding through high throughput sequencing (HTS). A total of 740 m3 of air were pumped through a 0.22 µm membrane. Snow obtained shortly after deposition was kept at room temperature and yielded 3.760 L of water, which was filtered using Sterivex membranes of 0.22 µm mesh size. The total DNA present was extracted and sequenced. We detected 171 fungal amplicon sequence variants (ASVs), 70 from the air and 142 from the snow. They were dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota and Mucoromycota. Pseudogymnoascus, Cladosporium, Mortierella and Penicillium sp. were the most dominant ASVs detected in the air in rank order. In snow, Cladosporium, Pseudogymnoascus, Penicillium, Meyerozyma, Lecidea, Malassezia, Hanseniaspora, Austroplaca, Mortierella, Rhodotorula, Penicillium, Thelebolus, Aspergillus, Poaceicola, Glarea and Lecanora were the dominant ASVs present. In general, the two fungal assemblages displayed high diversity, richness, and dominance indices, with the assemblage found in snow having the highest diversity indices. Of the total fungal ASVs detected, 29 were only present in the air sample and 101 in the snow sample, with only 41 present in both samples; however, when only the dominant taxa from both samples were compared none occurred only in the air and, among the rare portion, 26 taxa occurred in both air and snow. Application of HTS revealed the presence of a more diverse fungal community in the air and snow of Livingston Island in comparison with studies using traditional isolation methods. The assemblages were dominated by cold-adapted and cosmopolitan fungal taxa, including members of the genera Pseudogymnoascus, Malassezia and Rhodotorula, which include some taxa reported as opportunistic. Our results support the hypothesis that the presence of microbiota in the airspora indicates the possibility of dispersal around Antarctica in the air column. However, further aeromycology studies are required to understand the dynamics of fungal dispersal within and beyond Antarctica.

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