scholarly journals Nutrient dynamics and stream order influence microbial community patterns along a 2914 km transect of the Mississippi River

2016 ◽  
Author(s):  
Michael W. Henson ◽  
Jordan Hanssen ◽  
Greg Spooner ◽  
Patrick Fleming ◽  
Markus Pukonen ◽  
...  
Keyword(s):  
Water Quality ◽  
Microbial Community ◽  
Mississippi River ◽  
Nutrient Dynamics ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ohio River ◽  
Core Microbiome ◽  
Water Transportation ◽  
River Confluence

AbstractDraining 31 states and roughly 3 million km2, the Mississippi River (MSR) and its tributaries constitute an essential resource to millions of people for clean drinking water, transportation, agriculture, and industry. Since the turn of the 20thcentury, MSR water quality has continually rated poorly due to human activity. Acting as first responders, microorganisms can mitigate, exacerbate, and/or serve as predictors for water quality, yet we know little about their community structure or ecology at the whole river scale for large rivers. We collected both biological (16S and 18S rRNA gene amplicons) and physicochemical data from 38 MSR sites over nearly 3000 km from Minnesota to the Gulf of Mexico. Our results revealed a microbial community composed of similar taxa to other rivers but with unique trends in the relative abundance patterns among phyla, OTUs, and the core microbiome. Furthermore, we observed a separation in microbial communities that mirrored the transition from an 8thto 10thStrahler order river at the Missouri River confluence, marking a different start to the lower MSR than the historical distinction at the Ohio River confluence in Cairo, IL. Within MSR microbial assemblages we identified subgroups of OTUs from the phyla Acidobacteria, Bacteroidetes, Oomycetes, and Heterokonts that were associated with, and predictive of, the important eutrophication nutrients nitrate and phosphate. This study offers the most comprehensive view of MSR microbiota to date, provides important groundwork for higher resolution microbial studies of river perturbation, and identifies potential microbial indicators of river health related to eutrophication.

scholarly journals New insights into the influence of plant and microbial diversity on denitrification rates in a salt marsh

2020 ◽  
Author(s):  
Olivia U. Mason ◽  
Patrick Chanton ◽  
Loren N. Knobbe ◽  
Julian Zaugg ◽  
Behzad Mortazavi
Keyword(s):  
Microbial Community ◽  
Salt Marsh ◽  
Microbial Diversity ◽  
Ecosystem Functions ◽  
Juncus Roemerianus ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Marsh Vegetation ◽  
Core Microbiome ◽  
N Removal

AbstractCoastal salt marshes are some of the most productive ecosystems on Earth, providing numerous services such as soil carbon storage, flood protection and nutrient filtering, several of which are mediated by the sediment microbiome associated with marsh vegetation. Here, nutrient filtering (nitrate removal through denitrification) was examined by determining microbial community structure (16S rRNA gene iTag sequencing), diversity, denitrification rates and metabolic potential (assembled metagenomic sequences) in collocated patches of Spartina alterniflora (Spartina) and Juncus roemerianus (Juncus) sediments. The iTag data showed that diversity and richness in Spartina and Juncus sediment microbial communities were highly similar. However, microbial community evenness differed significantly, with the most even communities observed in Juncus sediments. Further, denitrification rates were significantly higher in Juncus compared to Spartina, suggesting oscillations in microbial abundances and in particular the core microbiome identified herein, along with plant diversity influence marsh nitrogen (N) removal. Amplicon and assembled metagenome sequences pointed to a potentially important, yet unappreciated Planctomycetes role in N removal in the salt marsh. Thus, perturbations, such as sea-level rise, that can alter marsh vegetation distribution could impact microbial diversity and may ultimately influence the ecologically important ecosystem functions the marsh sediment microbiome provides.

scholarly journals The cultivation of Pyropia haitanensis has important impacts on the seawater microbial community

2020 ◽  
Vol 32 (4) ◽  
pp. 2561-2573
Author(s):  
Wenlei Wang ◽  
Lei Wu ◽  
Kai Xu ◽  
Yan Xu ◽  
Dehua Ji ◽  
...  
Keyword(s):  
Microbial Community ◽  
Growth And Development ◽  
Alpha Diversity ◽  
18S Rrna Gene ◽  
Pyropia Haitanensis ◽  
Rrna Gene ◽  
Cultivation Period ◽  
Rrna Gene Sequencing ◽  
Bacteria And Fungi ◽  
Surrounding Seawater

Abstract Microorganisms play important roles in the growth and development of macroalgae. Still, the biodiversity of the epiphytic microbial community associated with the economically important red alga Pyropia haitanensis during the cultivation period remains uncharacterized, especially the effects of P. haitanensis cultivation on the microbial community of surrounding seawater. Here, we isolated epiphytic microbes from P. haitanensis during the thallus stage during oceanic cultivation and the conchocelis stage during industrial cultivation. The dynamic diversity patterns, as determined by 16S and 18S rRNA gene sequencing of the bacterial and fungal communities, respectively, associated with P. haitanensis and seawater in the presence and absence of algal cultivation were investigated. A notable distinction was observed between the microbial communities of seawater with and without P. haitanensis cultivation. Additionally, the alpha-diversity of seawater with P. haitanensis cultivation was significantly greater than without P. haitanensis cultivation. Cyanobacteria were the dominant species in the latter, while Rhodobacteraceae was enriched in the former. Furthermore, there were significant differences in the microbial community of P. haitanensis at the thallus and conchocelis stages. Seawater properties had significant direct effects on the microbial diversity of P. haitanensis and cultivation seawater, but not on non-cultivation seawater. The enriched microbial presence might promote thallus morphogenesis and be beneficial for the growth and development of both the thallus and conchocelis stages. These findings expand our knowledge of the bacteria and fungi that are beneficial for Pyropia nursery seeding and cultivation, as well as the effects of P. haitanensis cultivation on the seawater microbial community.

scholarly journals Methanogenic Granules Are Replicated, Whole Microbial Communities With Reproducible Responses To Environmental Cues

2020 ◽  
Author(s):  
Anna Christine Trego ◽  
Sarah O'Sullivan ◽  
Simon Mills ◽  
Estefania Porca ◽  
Christopher Quince ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Size Fraction ◽  
Methanogenic Archaea ◽  
Organic Content ◽  
Environmental Cues ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Methanogenic Activity ◽  
Fermentative Bacteria

Abstract Background In this study, individual anaerobic granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates originated from three different biomass sources, i.e. three different engineered biological wastewater treatment systems, were each size-separated into three fractions – small, medium and large – and characterised according to organic matter concentrations and rates of methanogenic activity. Differences in the microbial community structure of each size fraction from each source were determined using 16S rRNA gene sequencing. Subsequently, single granules from the large size fraction of one of the sources were separately subjected controlled environmental cues in novel micro batch reactors (mBRs). Results Organic content, methanogenic activity, and microbial community were significantly different between the three size fractions, with diversity trajectories replicated across the three sludge sources – indicating a potential development model as granules age. Individual large granules from one of these sources were statistically identical with respect to the structure of the active community based on cDNA analysis. It was observed that the active microbial community of individual granules, at the depth of 16S rRNA sequencing, produced reproducible responses to environmental conditions. While each condition resulted in the up-regulation of particular OTUs and clades, the core microbiome, consisting of many fermentative bacteria along with methanogenic archaea, namely, Methanosarcina and Methanobacterium , persisted. Conclusions At this level, single anaerobic granules can be considered highly-replicated whole-ecosystems, opening the door to high-throughput studies in Microbial Ecology.

scholarly journals Worldwide exploration of the microbiome harbored by the cnidarian model,Exaiptasia pallida(Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3235 ◽  
Author(s):  
Tanya Brown ◽  
Christopher Otero ◽  
Alejandro Grajales ◽  
Estefania Rodriguez ◽  
Mauricio Rodriguez-Lanetty
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Species ◽  
Sea Anemone ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Wide Range ◽  
Exaiptasia Pallida

Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemoneExaiptasia pallidashows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1–V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated withE. pallidaare broadly conserved across geographic space with samples, containing largelyProteobacteriaandBacteroides.However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgalSymbiodiniumsymbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact thatE. pallidais likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone modelE. pallidais the first global-scale study of its kind.

scholarly journals Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank

2016 ◽  
Author(s):  
Tanya Brown ◽  
Christopher Otero ◽  
Alejandro Grajales ◽  
Estefania Rodriguez ◽  
Mauricio Rodriguez-Lanetty
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Species ◽  
Sea Anemone ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Wide Range ◽  
Exaiptasia Pallida

Examination of host-microbe interactions in basal metazoans, such as cnidarians is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1-V4 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. These results contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. Instead, our findings suggest that environmental settings, not host specificity seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.

scholarly journals Distribution and diversity of eukaryotic microalgae in Kuwait waters assessed using 18S rRNA gene sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250645
Author(s):  
Vinod Kumar ◽  
Sabah Al Momin ◽  
Vanitha V. Kumar ◽  
Jasim Ahmed ◽  
Lamya Al-Musallam ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
18S Rrna ◽  
Biological Diversity ◽  
Marine Ecosystem ◽  
Distribution Patterns ◽  
Arid Environment ◽  
18S Rrna Gene ◽  
Anthropogenic Factors ◽  
Rrna Gene

The microbial communities play a crucial role in ecosystem functioning through interactions among individuals and taxonomic groups in a highly dynamic marine ecosystem. The structure and functioning of the microbial communities are often influenced by the changes in the surrounding environment. Monitoring the microbial diversity of the marine ecosystem helps to understand spatial patterns of microbial community and changes due to season, climate, and various drivers of biological diversity. Kuwait is characterized by an arid environment with a high degree of temperature variation during summer and winter. Our understanding of spatial distribution patterns of microbial communities, their diversity, and the influence of human activities on the degree of changes in the diversity of the microbial community in Kuwait territorial waters remain unclear. In this study, we employed 18S rRNA sequencing to explore marine microalgal community composition and dynamics in seawater samples collected from Kuwait waters over two seasonal cycles across six locations. A total of 448,184 sequences across 36 replicates corresponding to 12 samples from six stations were obtained. The quality-filtered sequences were clustered into 1,293 representative sequences, which were then classified into different eukaryotic taxa. This study reveals that the phytoplankton community in Kuwait waters is diverse and shows significant variations among different taxa during summer and winter. Dinoflagellates and diatoms were the most abundant season-dependent microalgae taxa in Kuwait waters. Alexandrium and Pyrophacus were abundant in summer, whereas Gonyaulax was abundant during the winter. The abundance of Coscinodiscus and Navicula, of the diatom genera, were also dependent upon both seasonal and possible anthropogenic factors. Our results demonstrate the effectiveness of a sequencing-based approach, which could be used to improve the accuracy of quantitative eukaryotic microbial community profiles.

scholarly journals Improved 18S and 28S rDNA primer sets for NGS-based parasite detection

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Asuka Kounosu ◽  
Kazunori Murase ◽  
Akemi Yoshida ◽  
Haruhiko Maruyama ◽  
Taisei Kikuchi
Keyword(s):  
Microbial Community ◽  
Polymerase Chain Reaction Amplification ◽  
18S Rrna Gene ◽  
28S Rdna ◽  
Rrna Gene ◽  
Parasite Detection ◽  
Eukaryotic Species ◽  
High Throughput Detection ◽  
Primer Sets ◽  
Next Generation Sequencing Ngs

Abstract The development and application of next-generation sequencing (NGS) have enabled comprehensive analyses of the microbial community through extensive parallel sequencing. Current analyses of the eukaryotic microbial community are primarily based on polymerase chain reaction amplification of 18S rRNA gene (rDNA) fragments. We found that widely-used 18S rDNA primers can amplify numerous stretches of the bacterial 16S rRNA gene, preventing the high-throughput detection of rare eukaryotic species, particularly in bacteria-rich samples such as faecal material. In this study, we employed in silico and NGS-based analyses of faecal samples to evaluated the existing primers targeting eukaryotic 18S and 28S rDNA in terms of avoiding bacterial read contamination and improving taxonomic coverage for eukaryotes, with a particular emphasis on parasite taxa. Our findings revealed that newly selected primer sets could achieve these objectives, representing an alternative strategy for NGS.

Fishery Resources, Environment, and Conservation in the Mississippi and Yangtze (Changjiang) River Basins

2016 ◽  
Keyword(s):  
Gulf Of Mexico ◽  
Mississippi River ◽  
Fish Fauna ◽  
Missouri River ◽  
River Basins ◽  
Nonnative Species ◽  
Habitat Alteration ◽  
Ohio River ◽  
Changjiang River ◽  
River Confluence

<em>Abstract</em>.—This chapter provides a listing of fishes known to be present in the Mississippi River from the headwaters at Lake Itasca, Minnesota to the Gulf of Mexico terminus. A total of 188 species are presently known from the Mississippi River, including 3 diadromous species and 17 nonnative species that have established self-sustaining populations in one or more reaches of the Mississippi River. Species are classified into three relative abundance categories and noted as residents, peripherals, introduced (established nonnatives), or strays (introduced but not established). The diversity of fishes varies longitudinally with 78 species in the reach from the headwaters to St. Anthony Falls; 113 and 105 species in the upper (Upper St. Anthony Lock and Dam to Pool 13) and lower (Pools 14–26) impounded reaches, respectively; and 121 and 136 species in the upper (Missouri River confluence to Ohio River confluence) and lower (Ohio River to the Gulf of Mexico outlet) free-flowing reaches, respectively. Although the composition of the Mississippi River fish fauna has changed little despite more than 80 years of habitat alteration, the extirpation of five species in individual reaches of the river may be a forewarning of a system losing resiliency and indicate the need for habitat conservation and rehabilitation to conserve the biodiversity of North America’s largest river.

scholarly journals Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank

2016 ◽  
Author(s):  
Tanya Brown ◽  
Christopher Otero ◽  
Alejandro Grajales ◽  
Estefania Rodriguez ◽  
Mauricio Rodriguez-Lanetty
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Species ◽  
Sea Anemone ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Wide Range ◽  
Exaiptasia Pallida

Examination of host-microbe interactions in basal metazoans, such as cnidarians is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1-V4 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. These results contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. Instead, our findings suggest that environmental settings, not host specificity seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.

scholarly journals Gastrointestinal Segments Influenced Fermentation End-Products, Microbiota and Microbial Abundances in Goats

2021 ◽  
Author(s):  
Tsegay Gebremariam ◽  
Zhiliang Tan
Keyword(s):  
Fatty Acids ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Copies ◽  
End Products ◽  
The Impact

Abstract Purpose: Carbohydrate diets altered fermentation end-products and microbial community in the gastrointestinal tracts (GIT) of goats. Gastrointestinal contents used to determine the impact of carbohydrate feeds on fermentation end-products and microbial community in goats.Methodology: in the study goats were assigned to one of the two treatments corn meal (CM) or Corn gluten (CG) in a randomized block design (400 g/kg DM each). Goats were slaughtered, GIT liquids were used to determine dissolved gasses, fatty acids and microbial community.Results: Goats fed CG increased molar acetate (P < 0.05), lowered butyrate and propionate in the fore and hindgut comparing to those goats received CM. Goats received CM had higher (P < 0.05) dH2 while lowered dH2S in the fore and hindgut than those goats fed with CG treatment. The fore and hindgut had higher (P < 0.01) 16S rRNA gene copies of bacteria, protozoa, methanogens and 18S rRNA gene copies fungi than in the ileum and cecum. Goats fed CG diet had higher (P < 0.05)16S rRNA gene copies of bacteria, protozoa, methanogens, and 18S rRNA gene copies of fungi than those goats fed with CM diet. Conclusion fore and hindguts improved dissolved gasses, fatty acids and microbial community comparing with in the ileum and cecum. Goats fed CM had improved the Methanobacterials order and Methanobrevibacter genus as compared with those goats fed CG. The study suggested that hindgut segments have a reasonable contribution as foregut to methane emissions from goats.

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