Composition of seagrass phyllosphere microbial communities suggests rapid environmental regulation of community structure

2021 ◽  
Author(s):  
Margaret A Vogel ◽  
Olivia U Mason ◽  
Thomas E Miller
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Host Plant ◽  
Environmental Conditions ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Community Members ◽  
Bacterial Phyla ◽  
Primary Driver ◽  
Rrna Gene Sequencing

Abstract Recent studies have revealed that seagrass blade surfaces, also known as the phyllosphere, are rich habitats for microbes; however, the primary drivers of composition and structure in these microbial communities are largely unknown. This study utilized a reciprocal transplant approach between two sites with different environmental conditions combined with 16S rRNA gene sequencing (iTag) to examine the relative influence of environmental conditions and host plant on phyllosphere community composition of the seagrass Thalassia testudinum. After thirty days, identity of phyllosphere microbial community members was more similar within the transplant sites than between despite differences in the source of host plant. Additionally, the diversity and evenness of these communities was significantly different between the two sites. These results indicated that local environmental conditions can be a primary driver in structuring seagrass phyllosphere microbial communities over relatively short time scales. Composition of microbial community members in this study also deviated from those in previous seagrass phyllosphere studies with a higher representation of candidate bacterial phyla and archaea than previously observed. The capacity for seagrass phyllosphere microbial communities to shift dramatically with environmental conditions, including ecosystem perturbations, could significantly affect seagrass-microbe interactions in ways that may influence the health of the seagrass host.

scholarly journals Spatially-resolved correlative microscopy and microbial identification reveals dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment

2020 ◽  
Author(s):  
Jeffrey Marlow ◽  
Rachel Spietz ◽  
Keun-Young Kim ◽  
Mark Ellisman ◽  
Peter Girguis ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Microbial Communities ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Community Members ◽  
Marsh Sediment ◽  
Anabolic Activity ◽  
Salt Marsh Sediment ◽  
Rrna Gene Sequencing ◽  
And Function

AbstractCoastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were embedded and analyzed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ∼60% in the top cm to 10-25% between 2-7 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase, and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.Statement of SignificanceMicroscale spatial relationships dictate critical aspects of a microbiome’s inner workings and emergent properties, such as evolutionary pathways, niche development, and community structure and function. However, many commonly used methods in microbial ecology neglect this parameter – obscuring important microbe-microbe and microbe-mineral interactions – and instead employ bulk-scale methodologies that are incapable of resolving these intricate relationships.This benchmark study presents a compelling new approach for exploring the anabolic activity of a complex microbial community by mapping the precise spatial configuration of anabolically active organisms within mineralogically heterogeneous sediment through in situ incubation, resin embedding, and correlative fluorescence and electron microscopy. In parallel, active organisms were identified through fluorescence-activated cell sorting and 16S rRNA gene sequencing, enabling a powerful interpretive framework connecting location, identity, activity, and putative biogeochemical roles of microbial community members.We deploy this novel approach in salt marsh sediment, revealing quantitative insights into the fundamental principles that govern the structure and function of sediment-hosted microbial communities. In particular, at different sediment horizons, we observed striking changes in the proportion of anabolically active cells, the identities of the most prominent active community members, and the nature of microbe-mineral affiliations. Improved approaches for understanding microscale ecosystems in a new light, such as those presented here, reveal environmental parameters that promote or constrain metabolic activity and clarify the impact that microbial communities have on our world.

Analysis of changes in the microbial community structure and physicochemical properties during the fermentation of sand crab juice

2021 ◽  
Author(s):  
Meiyan Luo ◽  
Leilei Chen ◽  
Huanming Liu ◽  
Jiahui Jiang ◽  
Chongxi Lai ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Isolation Technique ◽  
Bacterial Phyla ◽  
Staphylococcus Equorum ◽  
Rrna Gene Sequencing

Abstract The structure of the microbial community during sand crab juice fermentation was analyzed using culture-based methods and high-throughput 16S rRNA gene sequencing. Additionally, the changes in amino acid nitrogen (AAN) and total volatile basic nitrogen (TVB-N) were evaluated. Staphylococcus equorum, Staphylococcus arlettae, Staphylococcus saprophyticus, Salinicoccus amylolyticus, and Bacillus cereus were isolated by traditional culture isolation technique. The Good's coverage obtained by high-throughput sequencing was over 99.5%, and the Chao1 and Simpson indices showed small fluctuations, indicating that the species abundance and diversity did not change significantly during the fermentation process, although the abundance decreased. Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the dominant bacterial phyla observed during fermentation, whereas Aquabacterium, Roseovarius, Muribaculaceae, and Silicimonas were the dominant bacterial genera. The AAN content increased from 0.15 to 0.43 g/100 mL during the 15-day fermentation, indicating the production of small peptides and amino acids during fermentation. The TVB-N content (25.2 mg/100 mL) on day 15 indicated slight spoilage of sand crab juice, although the freshness conformed to the production standard. These results provide a theoretical basis for improving the quality and optimizing the production process of sand crab juice.

scholarly journals Dynamics of Soil Microbial Communities During Diazepam and Oxazepam Biodegradation in Soil Flooded by Water From a WWTP

2021 ◽  
Vol 12 ◽  
Author(s):  
Marc Crampon ◽  
Coralie Soulier ◽  
Pauline Sidoli ◽  
Jennifer Hellal ◽  
Catherine Joulian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Treated Wastewater ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Rrna Gene Sequencing

The demand for energy and chemicals is constantly growing, leading to an increase of the amounts of contaminants discharged to the environment. Among these, pharmaceutical molecules are frequently found in treated wastewater that is discharged into superficial waters. Indeed, wastewater treatment plants (WWTPs) are designed to remove organic pollution from urban effluents but are not specific, especially toward contaminants of emerging concern (CECs), which finally reach the natural environment. In this context, it is important to study the fate of micropollutants, especially in a soil aquifer treatment (SAT) context for water from WWTPs, and for the most persistent molecules such as benzodiazepines. In the present study, soils sampled in a reed bed frequently flooded by water from a WWTP were spiked with diazepam and oxazepam in microcosms, and their concentrations were monitored for 97 days. It appeared that the two molecules were completely degraded after 15 days of incubation. Samples were collected during the experiment in order to follow the dynamics of the microbial communities, based on 16S rRNA gene sequencing for Archaea and Bacteria, and ITS2 gene for Fungi. The evolution of diversity and of specific operating taxonomic units (OTUs) highlighted an impact of the addition of benzodiazepines, a rapid resilience of the fungal community and an evolution of the bacterial community. It appeared that OTUs from the Brevibacillus genus were more abundant at the beginning of the biodegradation process, for diazepam and oxazepam conditions. Additionally, Tax4Fun tool was applied to 16S rRNA gene sequencing data to infer on the evolution of specific metabolic functions during biodegradation. It finally appeared that the microbial community in soils frequently exposed to water from WWTP, potentially containing CECs such as diazepam and oxazepam, may be adapted to the degradation of persistent contaminants.

scholarly journals Adaptation of Microbial Communities to Environmental Arsenic and Selection of Arsenite-Oxidizing Bacteria From Contaminated Groundwaters

2021 ◽  
Vol 12 ◽  
Author(s):  
Sarah Zecchin ◽  
Simona Crognale ◽  
Patrizia Zaccheo ◽  
Stefano Fazi ◽  
Stefano Amalfitano ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Inorganic Arsenic ◽  
16S Rrna Gene Sequencing ◽  
Northern Italy ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Main Driver ◽  
Rrna Gene Sequencing ◽  
Arsenite Oxidizing Bacteria ◽  
Card Fish

Arsenic mobilization in groundwater systems is driven by a variety of functionally diverse microorganisms and complex interconnections between different physicochemical factors. In order to unravel this great ecosystem complexity, groundwaters with varying background concentrations and speciation of arsenic were considered in the Po Plain (Northern Italy), one of the most populated areas in Europe affected by metalloid contamination. High-throughput Illumina 16S rRNA gene sequencing, CARD-FISH and enrichment of arsenic-transforming consortia showed that among the analyzed groundwaters, diverse microbial communities were present, both in terms of diversity and functionality. Oxidized inorganic arsenic [arsenite, As(III)] was the main driver that shaped each community. Several uncharacterized members of the genus Pseudomonas, putatively involved in metalloid transformation, were revealed in situ in the most contaminated samples. With a cultivation approach, arsenic metabolisms potentially active at the site were evidenced. In chemolithoautotrophic conditions, As(III) oxidation rate linearly correlated to As(III) concentration measured at the parental sites, suggesting that local As(III) concentration was a relevant factor that selected for As(III)-oxidizing bacterial populations. In view of the exploitation of these As(III)-oxidizing consortia in biotechnology-based arsenic bioremediation actions, these results suggest that contaminated aquifers in Northern Italy host unexplored microbial populations that provide essential ecosystem services.

scholarly journals Arsenic mobilization in a high arsenic groundwater revealed by metagenomic and Geochip analyses

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Zhou Jiang ◽  
Ping Li ◽  
Yanhong Wang ◽  
Han Liu ◽  
Dazhun Wei ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Arsenic Mobilization ◽  
Rrna Gene Sequencing ◽  
High Arsenic ◽  
High Arsenic Groundwater

Abstract Microbial metabolisms of arsenic, iron, sulfur, nitrogen and organic matter play important roles in arsenic mobilization in aquifer. In this study, microbial community composition and functional potentials in a high arsenic groundwater were investigated using integrated techniques of RNA- and DNA-based 16S rRNA gene sequencing, metagenomic sequencing and functional gene arrays. 16S rRNA gene sequencing showed the sample was dominated by members of Proteobacteria (62.3–75.2%), such as genera of Simplicispira (5.7–6.7%), Pseudomonas (3.3–5.7%), Ferribacterium (1.6–4.4%), Solimonas (1.8–3.2%), Geobacter (0.8–2.2%) and Sediminibacterium (0.6–2.4%). Functional potential analyses indicated that organics degradation, assimilatory sulfate reduction, As-resistant pathway, iron reduction, ammonification, nitrogen fixation, denitrification and dissimilatory nitrate reduction to ammonia were prevalent. The composition and function of microbial community and reconstructed genome bins suggest that high level of arsenite in the groundwater may be attributed to arsenate release from iron oxides reductive dissolution by the iron-reducing bacteria, and subsequent arsenate reduction by ammonia-producing bacteria featuring ars operon. This study highlights the relationship between biogeochemical cycling of arsenic and nitrogen in groundwater, which potentially occur in other aquifers with high levels of ammonia and arsenic.

scholarly journals Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys

2020 ◽  
Author(s):  
Ravichandra Vemuri ◽  
Chrissy Sherrill ◽  
Matthew A Davis ◽  
Kylie Kavanagh
Keyword(s):  
Microbial Community ◽  
Systemic Inflammation ◽  
16S Rrna Gene Sequencing ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Vervet Monkeys ◽  
Fecal Samples ◽  
Age Related ◽  
Rrna Gene Sequencing ◽  
The Stability

Abstract Age-related changes in gut microbiome impact host health. The interactive relationship between the microbiome and physiological systems in an aged body system remains to be clearly defined, particularly in the context of inflammation. Therefore, we aimed to evaluate systemic inflammation, microbial translocation (MT), and differences between fecal and mucosal microbiomes. Ascending colon mucosal biopsies, fecal samples, and blood samples from healthy young and old female vervet monkeys were collected for 16S rRNA gene sequencing, MT, and cytokine analyses, respectively. To demonstrate microbial co-occurrence patterns, we used Kendall’s tau correlation measure of interactions between microbes. We found elevated levels of plasma LBP-1, MCP-1, and CRP in old monkeys, indicative of higher MT and systemic inflammation. Microbiome analysis revealed significant differences specific to age. At the phylum level, abundances of pathobionts such as Proteobacteria were increased in the mucosa of old monkeys. At the family level, Helicobacteriaceae was highly abundant in mucosal samples (old); in contrast, Ruminococcaceae were higher in the fecal samples of old monkeys. We found significantly lower Firmicutes:Bacteroidetes ratio and lower abundance of butyrate-producing microbes in old monkeys, consistent with less healthy profiles. Microbial community co-occurrence analysis on mucosal samples revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys. Our findings provide novel insights into systemic inflammation and gut microbial interactions, highlight the importance of the mucosal niche, and facilitate further understanding of the decline in the stability of the microbial community with aging.

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Alexander Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

scholarly journals Impact of Diabetes on the Gut and Salivary IgA Microbiomes

2020 ◽  
Vol 88 (12) ◽  
Author(s):  
Eric L. Brown ◽  
Heather T. Essigmann ◽  
Kristi L. Hoffman ◽  
Noah W. Palm ◽  
Sarah M. Gunter ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Immunoglobulin A ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Host Immune Responses ◽  
Mucosal Surfaces ◽  
Immune Mediated ◽  
Rrna Gene Sequencing ◽  
Immune Exclusion

ABSTRACT Mucosal surfaces like those present in the lung, gut, and mouth interface with distinct external environments. These mucosal gateways are not only portals of entry for potential pathogens but also homes to microbial communities that impact host health. Secretory immunoglobulin A (SIgA) is the single most abundant acquired immune component secreted onto mucosal surfaces and, via the process of immune exclusion, shapes the architecture of these microbiomes. Not all microorganisms at mucosal surfaces are targeted by SIgA; therefore, a better understanding of the SIgA-coated fraction may identify the microbial constituents that stimulate host immune responses in the context of health and disease. Chronic diseases like type 2 diabetes are associated with altered microbial communities (dysbiosis) that in turn affect immune-mediated homeostasis. 16S rRNA gene sequencing of SIgA-coated/uncoated bacteria (IgA-Biome) was conducted on stool and saliva samples of normoglycemic participants and individuals with prediabetes or diabetes (n = 8/group). These analyses demonstrated shifts in relative abundance in the IgA-Biome profiles between normoglycemic, prediabetic, or diabetic samples distinct from that of the overall microbiome. Differences in IgA-Biome alpha diversity were apparent for both stool and saliva, while overarching bacterial community differences (beta diversity) were also observed in saliva. These data suggest that IgA-Biome analyses can be used to identify novel microbial signatures associated with diabetes and support the need for further studies exploring these communities. Ultimately, an understanding of the IgA-Biome may promote the development of novel strategies to restructure the microbiome as a means of preventing or treating diseases associated with dysbiosis at mucosal surfaces.

scholarly journals The Gut Microbial Community of Antarctic Fish Detected by 16S rRNA Gene Sequence Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Wei Song ◽  
Lingzhi Li ◽  
Hongliang Huang ◽  
Keji Jiang ◽  
Fengying Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Antarctic Fish ◽  
16S Rrna Gene Sequencing ◽  
Physiological Characteristics ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community

Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and a range of fitness in fish, but little is known about the gut microbial community in Antarctic fish. In this study, the composition of intestinal microbial community in four species of Antarctic fish was detected based on 16S rRNA gene sequencing. As a result, 1 004 639 sequences were obtained from 13 samples identified into 36 phyla and 804 genera, in which Proteobacteria, Actinobacteria, Firmicutes, Thermi, and Bacteroidetes were the dominant phyla, and Rhodococcus, Thermus, Acinetobacter, Propionibacterium, Streptococcus, and Mycoplasma were the dominant genera. The number of common OTUs (operational taxonomic units) varied from 346 to 768, while unique OTUs varied from 84 to 694 in the four species of Antarctic fish. Moreover, intestinal bacterial communities in individuals of each species were not really similar, and those in the four species were not absolutely different, suggesting that bacterial communities might influence the physiological characteristics of Antarctic fish, and the common bacterial communities might contribute to the fish survival ability in extreme Antarctic environment, while the different ones were related to the living habits. All of these results could offer certain information for the future study of Antarctic fish physiological characteristics.

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