scholarly journals Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs

2017 ◽  
Vol 83 (10) ◽  
Author(s):  
Christopher Staley ◽  
Thomas Kaiser ◽  
Maribeth L. Gidley ◽  
Ian C. Enochs ◽  
Paul R. Jones ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Coral Reefs ◽  
Microbial Communities ◽  
Treated Wastewater ◽  
Coral Tissue ◽  
Next Generation ◽  
Sources Of Pollution ◽  
Reef Communities ◽  
Coastal Inlet ◽  
Generation Sequencing

ABSTRACT Coral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine the relationships between microbial communities in these matrices and those in reef water and coral tissues. Significant differences in microbial communities were noted among all sample types but varied between sampling areas. Contamination from outfalls was found to be the greatest potential source of LBSP influencing native microbial community structure among all reef samples, although pollution from inlets was also noted. Notably, reef water and coral tissue communities were found to be more greatly impacted by LBSP at southern reefs, which also experienced the most degradation during the course of the study. The results of this study provide new insights into how microbial communities from LBSP can impact coral reefs in southeast Florida and suggest that wastewater outfalls may have a greater influence on the microbial diversity and structure of these reef communities than do contaminants carried in runoff, although the influences of runoff and coastal inlet discharge on coral reefs are still substantial. IMPORTANCE Coral reefs are known to be endangered due to sewage discharge and to runoff of nutrients, pesticides, and other substances associated with anthropogenic activity. Here, we used next-generation sequencing to characterize the microbial communities of potential contaminant sources in order to determine how environmental discharges of microbiota and their genetic material may influence the microbiomes of coral reef communities and coastal receiving waters. Runoff delivered through inlet discharges impacted coral microbial communities, but impacts from oceanic outfalls carrying treated wastewater were greater. Geographic differences in the degree of impact suggest that coral microbiomes may be influenced by the microbiological quality of treated wastewater.

Microbial Communities’ Characterization in Urban Recreational Surface Waters Using Next Generation Sequencing

2021 ◽  
Author(s):  
Laura Vega ◽  
Jesús Jaimes ◽  
Duvan Morales ◽  
David Martínez ◽  
Lissa Cruz-Saavedra ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Surface Waters ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

2017 ◽  
Author(s):  
Taha Soliman ◽  
Sung-Yin Yang ◽  
Tomoko Yamazaki ◽  
Holger Jenke-Kodama
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Soil Microbial Communities ◽  
Next Generation ◽  
Microbial Composition ◽  
Okinawa Island ◽  
The Impact ◽  
Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P <0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

scholarly journals Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

2017 ◽  
Author(s):  
Taha Soliman ◽  
Sung-Yin Yang ◽  
Tomoko Yamazaki ◽  
Holger Jenke-Kodama
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Soil Microbial Communities ◽  
Next Generation ◽  
Microbial Composition ◽  
Okinawa Island ◽  
The Impact ◽  
Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P <0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

scholarly journals Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4178 ◽  
Author(s):  
Taha Soliman ◽  
Sung-Yin Yang ◽  
Tomoko Yamazaki ◽  
Holger Jenke-Kodama
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Soil Microbial Communities ◽  
Next Generation ◽  
Microbial Composition ◽  
Okinawa Island ◽  
The Impact ◽  
Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil®DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin®Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA;P < 0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

scholarly journals Genomic characterization of fecal microbial communities in severely sick humans and broiler chickens using next generation sequencing

2020 ◽  
Author(s):  
Ome Kalsoom Afridi ◽  
Johar Ali ◽  
Jeong Ho Chang
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Broiler Chickens ◽  
Human Subjects ◽  
Fecal Microbiota ◽  
Next Generation ◽  
Microbial Association ◽  
Taxonomic Profiling ◽  
Microbial Dysbiosis ◽  
Generation Sequencing

Abstract Background: Microbiota plays an important role in food safety and its alteration poses a serious threat to humans. Comparative microbiome profiling using next-generation sequencing (NGS) enabled the understanding of microbial diversity and similarity between different species. In this study, we used NGS to profile the fecal microbiota of sick human and broiler chickens. A total of 26 fecal samples were collected from severely sick human subjects (n= 13) and broiler chickens (n=13) with similar symptoms. Results: The total number of microbial species detected in broiler chickens fecal microbiota was higher than that of humans. Phylum Proteobacteria was the most abundant in both human and broiler chickens fecal microbiota while Tenericutes was found to be least abundant in both species. Phylum Actinobacteria was found only in the human fecal microbiota. In both humans and broiler chickens, E.coli was found to be phylogenetically related suggesting a microbial association between both species. Conclusion: NGS based taxonomic profiling revealed the association of microbial dysbiosis with extreme sickness in both humans and broiler chickens. The dominance of phylum Proteobacteria in both the species ascertains their altered gut microbiota. Both human and broiler chickens microbial communities were found to be genetically related indicating horizontal transfer of microbes between the two species.

scholarly journals The apical root canal system microbial communities determined by next-generation sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Luciana Carla Neves de Brito ◽  
Janet Doolittle-Hall ◽  
Chun-Teh Lee ◽  
Kevin Moss ◽  
Wilson Bambirra Júnior ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Root Canal ◽  
Next Generation ◽  
Canal System ◽  
Root Canal System ◽  
Generation Sequencing

scholarly journals Symbiodinium diversity and potential hybridisation on the highly biodiverse coral reefs of Timor-Leste

2021 ◽  
Author(s):  
◽  
Joshua Brian
Keyword(s):  
Next Generation Sequencing ◽  
Coral Reefs ◽  
Environmental Stress ◽  
Strong Evidence ◽  
Putative Hybrid ◽  
Its2 Region ◽  
Next Generation ◽  
Timor Leste ◽  
Clade C ◽  
Generation Sequencing

<p>To persist in oligotrophic waters, reef-building corals rely on nutritional interactions with their intracellular symbionts: photosynthetic dinoflagellates of the genus Symbiodinium. This relationship is threatened by increasing environmental stress, which can stimulate loss of these symbionts from coral tissues (‘coral bleaching’). Members of the genus Symbiodinium display high levels of genetic diversity, and demonstrate a corresponding diversity in physiological responses to environmental change. However, the true diversity and potential for genetic adaptation in this genus remain poorly characterised.  This thesis aimed to further the understanding of symbiont diversity and adaptive potential by conducting assessments of Symbiodinium at Atauro Island and the neighbouring Timor-Leste mainland. These sites have previously been shown to be of outstanding conservation value, with extremely high levels of coral diversity. Atauro Island also possibly hosts the highest diversity of reef fish in the world. However, the Symbiodinium communities at these sites have never been assessed. Two specific objectives were therefore addressed here. The first was to measure Symbiodinium diversity at Atauro Island (four sites) and Timor (three sites), using direct sequencing of three gene regions: cob gene, mitochondrion; ITS2 region, nucleus; and psbAncr region, chloroplast; in addition to Next Generation Sequencing of the ITS2 region. The second objective was to establish evidence for Symbiodinium hybridisation, a potentially rapid evolutionary mechanism that may facilitate adaptation to environmental stress, by looking for genetic incongruences between Symbiodinium organelles.  Coral symbionts of Timor-Leste were found to be similar to those from other coral reefs of the Indo-Pacific, with several host generalist and multiple host specific types observed. However, there were also several novel Symbiodinium types found (C15p, C15q, C1x, C1z). Despite their geographic proximity, there were strong differences observed between the symbiont communities of Atauro Island and mainland Timor. In particular, the coral genus Pocillopora hosted clade C symbionts exclusively at Atauro Island, while it hosted clade D exclusively at Timor sites. Other symbiont types also showed geographic partitioning, and diversity was 1.25 times higher at Atauro Island, a figure consistent for the cob and ITS2 regions. While Timor sites have comparable Symbiodinium diversity to other reefs globally, Atauro has noticeably elevated Symbiodinium diversity. Next Generation Sequencing affirmed these patterns, with Atauro Island sites having much more diverse cryptic populations of Symbiodinium, largely driven by symbionts in clade C. The exception was clade D symbionts, which were proportionally far more diverse at Timor, a pattern consistent in multiple coral genera.  There was strong evidence of genetic incongruence at two Atauro Island sites, with all testing procedures identifying genetic discordance between organellar and nuclear genomes, consistent with theoretical predictions of hybridisation. This study therefore presents strong evidence for Symbiodinium hybridisation, and its corroboration by multiple loci is significant. Putative hybrid Symbiodinium always had a common type as one of the possible parents, with a rarer symbiont as the other. For example, one putative hybrid had organellar genes of the common generalist Symbiodinium C40, while it was identified as the rare type C3z with the ITS2 region. Both of these Symbiodinium types were also found in congruent relationships, which strongly supports the possibility that they sexually reproduced to produce the incongruent putative hybrid.   Environmental stressors, such as increased temperature, turbidity and sedimentation, are suggested reasons for lowered Symbiodinium diversity at Timor, as they may impose a selection pressure on corals to only keep highly beneficial symbionts. This reduction in diversity likely limits the potential for adaptive change through methods like hybridisation, and highlights the need to assess and conserve symbiont diversity to the same extent as coral diversity.</p>

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