scholarly journals Bacterial Community Changes in Penaeus vannamei Boone, 1931 Surface and Rearing Water During Enterocytozoon hepatopenaei Infection

2021 ◽  
Vol 34 (2) ◽  
Author(s):  
PALLAVI BALIGA ◽  
◽  
PUNEETH THADOORU GOOLAPPA ◽  
MALATHI SHEKAR ◽  
S.K. GIRISHA ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Community Composition ◽  
Pond Water ◽  
Economic Losses ◽  
Penaeus Vannamei ◽  
Limited Information ◽  
Genetic Information Processing ◽  
Community Changes ◽  
Disease Indicators ◽  
Enterocytozoon Hepatopenaei

White faeces syndrome is one of the major disease problems in shrimp aquaculture, resulting in enormous economic losses to farmers. Although white faeces syndrome is usually associated with Enterocytozoon hepatopenaei (EHP) infections, it may not be the sole cause for the occurrence of white faecal strings on the pond water surface. There is limited information on the microbial dynamics in a pond affected by white faeces syndrome. Hence, this study aimed at the bacterial community changes occurring on the surface of shrimp Penaeus vannamei Boone, 1931 afflicted by the white faeces syndrome and the pond water in which it was reared. The pond water and the shrimp surface shared >45 % of the operational taxonomic units (OTUs), reflecting the influence of water quality on the bacterial community composition on the shrimp surface. Among these, the Proteobacteria formed the principal phyla and remained unaltered throughout the culture period. Bacteroidetes formed the second largest group across samples, followed by Cyanobacteria, Actinobacteria, Planctomycetes, Verrucomicrobia and Chloroflexi. The relative abundance levels of health indicator bacterial families such as Thiotrichaceae,Microbacteriaceae and Chitinophagaceae showed significant fluctuations on the shrimp surface. Disease indicators such as Rickettsiaceae, Mycobacteriaceae showed an increase in numbers on the shrimp surface. PICRUSt functional predictions revealed higher abundances of genes involved in metabolism and genetic information processing. The study provides valuable findings on the bacterial communities of rearing water and shrimp surface associated with white faeces syndrome.

scholarly journals Bacterial Communities Associated With Penaeus vannamei Boone, 1931 Surface and Its Rearing Water in Biofloc Culture System

2021 ◽  
Vol 34 (1) ◽  
Author(s):  
PALLAVI BALIGA ◽  
PUNEETH THADOORU GOOLAPPA ◽  
MALATHI SHEKAR ◽  
S.K. GIRISHA ◽  
RAMESH K.S. ◽  
...  
Keyword(s):  
Water Quality ◽  
Bacterial Community ◽  
Water Samples ◽  
Bacterial Communities ◽  
Culture System ◽  
Bacterial Community Composition ◽  
Pond Water ◽  
Penaeus Vannamei ◽  
Shrimp Culture ◽  
Surface Samples

The biofloc system is an ecologically sustainable shrimp culture system. The conglomerates of beneficial bacteria, algae and protozoa in pond water serve as a water quality management system and as a feed additive to the shrimps. This study aimed to characterise the microbial communities associated with the biofloc pond water and the surface of Penaeus vannamei Boone, 1931, reared in it using the Illumina Miseq sequencing technology. The multiple alpha diversity measures indicated the shrimp surface samples to be richer in diversity than the pond water samples. Analysis of the bacterial community revealed that Proteobacteria, Bacteroidetes, Planctomycetes and Cyanobacteria formed the principal phyla. There was a shift in the relative abundance of bacterial communities at each time point. The operational taxonomic units (OTU) analyses revealed that 18.38 % OTUs were shared by the pond water samples, the shrimp surface samples shared 29.35 % at the three different time points. PICRUST analysis revealed that the bacterial communities in the biofloc rearing water, and shrimp surface, were likely involved in intensive microbial metabolism and core housekeeping functions. The information generated will help understand the bacterial community composition associated with optimal water quality and shrimp health in a biofloc culture system.

scholarly journals Early life skin microbial trajectory as a function of vertical and environmental transmission in Bornean foam-nesting frogs

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sarah McGrath-Blaser ◽  
Morgan Steffen ◽  
T. Ulmar Grafe ◽  
María Torres-Sánchez ◽  
David S. McLeod ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Pond Water ◽  
Breeding Strategy ◽  
Skin Microbiome ◽  
Amphibian Skin ◽  
Environmental Interaction ◽  
Tadpole Skin ◽  
Foam Nest

Abstract Background The amphibian skin microbiome is an important mediator of host health and serves as a potential source of undiscovered scientifically significant compounds. However, the underlying modalities of how amphibian hosts obtain their initial skin-associated microbiome remains unclear. Here, we explore microbial transmission patterns in foam-nest breeding tree frogs from Southeast Asia (Genus: Polypedates) whose specialized breeding strategy allows for better delineation between vertically and environmentally derived microbes. To facilitate this, we analyzed samples associated with adult frog pairs taken after mating—including adults of each sex, their foam nests, environments, and tadpoles before and after environmental interaction—for the bacterial communities using DNA metabarcoding data (16S rRNA). Samples were collected from frogs in-situ in Brunei, Borneo, a previously unsampled region for amphibian-related microbial diversity. Results Adult frogs differed in skin bacterial communities among species, but tadpoles did not differ among species. Foam nests had varying bacterial community composition, most notably in the nests’ moist interior. Nest interior bacterial communities were discrete for each nest and overall displayed a narrower diversity compared to the nest exteriors. Tadpoles sampled directly from the foam nest displayed a bacterial composition less like the nest interior and more similar to that of the adults and nest exterior. After one week of pond water interaction the tadpole skin microbiome shifted towards the tadpole skin and pond water microbial communities being more tightly coupled than between tadpoles and the internal nest environment, but not to the extent that the skin microbiome mirrored the pond bacterial community. Conclusions Both vertical influence and environmental interaction play a role in shaping the tadpole cutaneous microbiome. Interestingly, the interior of the foam nest had a distinct bacterial community from the tadpoles suggesting a limited environmental effect on tadpole cutaneous bacterial selection at initial stages of life. The shift in the tadpole microbiome after environmental interaction indicates an interplay between underlying host and ecological mechanisms that drive community formation. This survey serves as a baseline for further research into the ecology of microbial transmission in aquatic animals.

scholarly journals Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators

Microbiome ◽  
2014 ◽  
Vol 2 (1) ◽  
pp. 32 ◽  
Author(s):  
Vaia Galimanas ◽  
Michael Hall ◽  
Natasha Singh ◽  
Michael David Lynch ◽  
Michael Goldberg ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Chronic Periodontitis ◽  
Bacterial Community Composition ◽  
Disease Indicators

Assessment of viral assemblages in different types of wetland water in northeast China using RAPD-PCR

2020 ◽  
Vol 85 ◽  
pp. 183-196
Author(s):  
Y Sun ◽  
J Liu ◽  
Q Yao ◽  
J Jin ◽  
X Liu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Water Samples ◽  
Northeast China ◽  
Bacterial Community Composition ◽  
Freshwater Wetlands ◽  
Viral Community ◽  
Rapd Pcr ◽  
Wetland Water ◽  
Different Types ◽  
Viral Communities

Viruses are the most abundant and ubiquitous biological entities in various ecosystems, yet few investigations of viral communities in wetlands have been performed. To address this data gap, water samples from 6 wetlands were randomly collected across northeast China; viruses in the water were concentrated by sequential tangential flow filtration, and viral communities were assessed through randomly amplified polymorphic DNA-PCR (RAPD-PCR) with 4 decamer oligonucleotide primers. Principal coordinate analysis and hierarchical clustering analysis of the DNA fingerprints showed that viral community compositions differed among the water samples: communities in the 2 coastal wetlands were more similar to each other than to those in the 4 freshwater wetlands. The Shannon-Weaver index (H) and evenness index (E) of the RAPD-PCR fingerprint also differed among the 6 wetlands. Mantel test revealed that the changes in viral communities in wetland water were most closely related to the water NH4+-N and inorganic C content, followed by total K, P, C and NO3--N. DNA sequence analysis of the excised bands revealed that viruses accounted for ~40% of all sequences. Among the hit viral homologs, the majority belonged to the Microviridae. Moreover, variance partitioning analysis showed that the viral community contributed 24.58% while environmental factors explained 30.56% of the bacterial community variation, indicating that the bacterial community composition was strongly affected by both viral community and water variables. This work provides an initial outline of the viral communities from different types of wetlands in northeast China and improves our understanding of the viral diversity in these ecosystems.

scholarly journals Collection of Environmental Variables and Bacterial Community Compositions in Marian Cove, Antarctica, during Summer 2018

Data ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 27
Author(s):  
Hyo-Ryeon Kim ◽  
Jae-Hyun Lim ◽  
Ju-Hyoung Kim ◽  
Il-Nam Kim
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Marine Bacteria ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Bacterial Community Composition ◽  
Composition Data ◽  
Decomposition Of Organic Matter ◽  
Class Level ◽  
Earth’S Climate

Marine bacteria, which are known as key drivers for marine biogeochemical cycles and Earth’s climate system, are mainly responsible for the decomposition of organic matter and production of climate-relevant gases (i.e., CO₂, N₂O, and CH₄). However, research is still required to fully understand the correlation between environmental variables and bacteria community composition. Marine bacteria living in the Marian Cove, where the inflow of freshwater has been rapidly increasing due to substantial glacial retreat, must be undergoing significant environmental changes. During the summer of 2018, we conducted a hydrographic survey to collect environmental variables and bacterial community composition data at three different layers (i.e., the seawater surface, middle, and bottom layers) from 15 stations. Of all the bacterial data, 17 different phylum level bacteria and 21 different class level bacteria were found and Proteobacteria occupy 50.3% at phylum level following Bacteroidetes. Gammaproteobacteria and Alphaproteobacteria, which belong to Proteobacteria, are the highest proportion at the class level. Gammaproteobacteria showed the highest relative abundance in all three seawater layers. The collection of environmental variables and bacterial composition data contributes to improving our understanding of the significant relationships between marine Antarctic regions and marine bacteria that lives in the Antarctic.

scholarly journals Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Danijela Šantić ◽  
Kasia Piwosz ◽  
Frano Matić ◽  
Ana Vrdoljak Tomaš ◽  
Jasna Arapov ◽  
...  
Keyword(s):  
Neural Network ◽  
Network Analysis ◽  
Bacterial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Adriatic Sea ◽  
Bacterial Community Composition ◽  
Environmental Data ◽  
Large Contribution ◽  
Neural Network Analysis

AbstractBacteria are an active and diverse component of pelagic communities. The identification of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profile, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classified the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more differentiated by depth than by area, with temperature and identified salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identified genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium-related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors affecting picoplankton in the open sea environment.

scholarly journals The effect of salinity on enterocytozoon hepatopenaei infection in Penaeus vannamei under experimental conditions

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
L. F. Aranguren Caro ◽  
F. Alghamdi ◽  
K. De Belder ◽  
J. Lin ◽  
H. N. Mai ◽  
...  
Keyword(s):  
Penaeus Monodon ◽  
Oral Route ◽  
Western Hemisphere ◽  
Penaeus Vannamei ◽  
Asian Countries ◽  
Experimental Conditions ◽  
Reliable Source ◽  
Specific Pathogen ◽  
Enterocytozoon Hepatopenaei ◽  
First Time

Abstract Background Enterocytozoon hepatopenaei (EHP) is an enteric pathogen that affects Penaeus vannamei and Penaeus monodon shrimp in many SE Asian countries. In the western hemisphere, EHP was reported for the first time in 2016 in farmed P. vannamei in Venezuela. Anecdotal evidence suggests that EHP is more prevalent in grow-out ponds where the salinity is high (> 15 parts per thousand (ppt)) compared to grow-out ponds with low salinities (< 5 ppt). Considering that P. vannamei is an euryhaline species, we were interested in knowing if EHP can propagate in P. vannamei in low salinities. Results In this study, we described an experimental infection using fecal strings as a source inoculum. Specific Pathogen Free (SPF) P. vannamei were maintained at three different salinities (2 ppt, 15 ppt, and 30 ppt) while continuously challenged using feces from known EHP-infected P. vannamei over a period of 3 weeks. The fecal strings, used as a source of EHP inocula in the challenges, was sufficient to elicit an infection in shrimp maintained at the three salinities. The infectivity of EHP in shrimp reared at 2 ppt, 15 ppt, and 30 ppt salinities was confirmed by PCR and histopathology. The prevalence and the severity of the EHP infection was higher at 30 ppt than at 2 ppt and 15 ppt. Conclusion The data suggests that fecal strings are a reliable source of EHP inoculum to conduct experimental challenges via the fecal-oral route. An EHP infection can occur at a salinity as low as 2 ppt, however, the prevalence and the severity of the EHP infection is higher at a salinity of 30 ppt.

scholarly journals Soil Bacterial Community Diversity and Composition as Affected by Tillage Intensity Treatments in Corn-Soybean Production Systems

2021 ◽  
Vol 12 (1) ◽  
pp. 157-172
Author(s):  
Shankar G. Shanmugam ◽  
Normie W. Buehring ◽  
Jon D. Prevost ◽  
William L. Kingery
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Production System ◽  
Soil Microbial Community ◽  
Production Systems ◽  
Bacterial Community Composition ◽  
Soybean Production ◽  
Soil Microbial ◽  
Soil Bacterial

Our understanding on the effects of tillage intensity on the soil microbial community structure and composition in crop production systems are limited. This study evaluated the soil microbial community composition and diversity under different tillage management systems in an effort to identify management practices that effectively support sustainable agriculture. We report results from a three-year study to determine the effects on changes in soil microbial diversity and composition from four tillage intensity treatments and two residue management treatments in a corn-soybean production system using Illumina high-throughput sequencing of 16S rRNA genes. Soil samples were collected from tillage treatments at locations in the Southern Coastal Plain (Verona, Mississippi, USA) and Southern Mississippi River Alluvium (Stoneville, Mississippi, USA) for soil analysis and bacterial community characterization. Our results indicated that different tillage intensity treatments differentially changed the relative abundances of bacterial phyla. The Mantel test of correlations indicated that differences among bacterial community composition were significantly influenced by tillage regime (rM = 0.39, p ≤ 0.0001). Simpson’s reciprocal diversity index indicated greater bacterial diversity with reduction in tillage intensity for each year and study location. For both study sites, differences in tillage intensity had significant influence on the abundance of Proteobacteria. The shift in the soil bacterial community composition under different tillage systems was strongly correlated to changes in labile carbon pool in the system and how it affected the microbial metabolism. This study indicates that soil management through tillage intensity regime had a profound influence on diversity and composition of soil bacterial communities in a corn-soybean production system.

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