scholarly journals Assessment of total bacterial diversity in whiteleg shrimps and its aquaculture environment in Pangkajene and Banyuwangi, Indonesia

2021 ◽  
pp. 26-37
Author(s):  
Yuni Puji Hastuti ◽  
Yuli Siti Fatma ◽  
Hardi Pitoyo ◽  
Wildan Nurussalam ◽  
Jajang Ruhyana
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Community Structure ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Composition ◽  
Sequencing Platform ◽  
The Difference

Detection of bacterial diversity in whiteleg shrimps and its rearing water is a vital first step in monitoring aquaculture activities. Bacterial community imbalance in whiteleg shrimps and its rearing water influences the quality and quantity of shrimp production. Identifying the bacterial community provides basic information related to dominant bacterial groups in whiteleg shrimps and environments, providing recommendations for proper environmental monitoring and management. In this study, we investigated bacterial community structure in the rearing water and intestinal tract of whiteleg shrimp (Litopenaeus vannamei) collected from two sites, i.e., Pangkajene, South Sulawesi (SU) and Banyuwangi, East Java (BW), Indonesia. The bacterial community was analyzed using amplicon sequencing with Illumina sequencing platform based on the V3-V4 region of the 16S rRNA genes. Bacterial diversity and composition were found differed between the rearing water and the shrimps’ intestines. Bacterial diversity in the rearing water of Banyuwangi (W.BW) was higher than that of Pangkajene (W.SU). Proteobacteria, Bacteroidetes, and Firmicutes were found as the most dominant phyla in rearing water from both farms, while distinct bacterial composition was observed in the shrimps’ intestines. The shrimp intestine from Banyuwangi (U.BW) was dominated by Firmicutes (22.36%), Proteobacteria (22.33%), and Verrucomicrobia (21.11%). In contrast, the shrimp intestine from Pangkajene (U.SU) was highly dominated by Tenericutes (88.54%), followed by Proteobacteria (4.66%), and Firmicutes (2.27%). The difference in bacterial community structure between the rearing water and shrimps’ intestines suggested that the host intestinal environment might have greater selective pressure for bacterial composition inhabiting L.vannamei intestines. Our observations suggest that the shrimps cultured in the rearing water with the similar dominant bacterial group have specific intestinal bacterial diversity.

scholarly journals Response of bacterioplankton community structure to an artificial gradient of <i>p</i>CO<sub>2</sub> in the Arctic Ocean

2012 ◽  
Vol 9 (8) ◽  
pp. 10645-10668 ◽  
Author(s):  
R. Zhang ◽  
X. Xia ◽  
S. C. K. Lau ◽  
C. Motegi ◽  
M. G. Weinbauer ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
Bacterial Community ◽  
Ocean Acidification ◽  
Bacterial Diversity ◽  
Bacterial Community Structure ◽  
Total Alkalinity ◽  
16S Rrna Genes ◽  
The Arctic ◽  
Rrna Genes

Abstract. The influences of ocean acidification on bacterial diversity were investigated using DNA fingerprinting and clone library analysis of bacterioplankton samples collected from the largest CO2 manipulation mesocosm study that had been performed thus far. Terminal restriction fragment length polymorphism analysis of the PCR amplicons of the 16S rRNA genes revealed that bacterial diversity, species richness and community structure varied with the time of incubation but not the degree of ocean acidification. The phylogenetic composition of the major bacterial assemblage after a 30-day incubation under various pCO2 concentrations did not show clear effects of pCO2 levels. However, the maximum apparent diversity and species richness which occurred during incubation differed in the high and low pCO2 treatments, in which different bacterial community structure harbored. In addition, total alkalinity was one of the contributing factors for the temporal variations in bacterial community structure observed during incubation. A negative relationship between the relative abundance of Bacteroidetes and pCO2 levels was observed for samples at the end of the experiment. Our study suggested that ocean acidification affected the development of bacterial assemblages and potentially impacts the ecological function of the bacterioplankton in the marine ecosystem.

scholarly journals Diet is not the primary driver of bacterial community structure in the gut of litter-feeding cockroaches

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Niclas Lampert ◽  
Aram Mikaelyan ◽  
Andreas Brune
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Community Structure ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Feeding Groups ◽  
Reducing Conditions ◽  
Primary Driver

Abstract Background Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter. Results The physicochemical conditions determined with microsensors in the guts of Ergaula capucina, Pycnoscelus surinamensis, and Byrsotria rothi were similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop of B. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood-feeding higher termites. Conclusion Our results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.

scholarly journals Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

2013 ◽  
Vol 32 (1) ◽  
pp. 17390 ◽  
Author(s):  
Annette K. Møller ◽  
Ditte A. Søborg ◽  
Waleed Abu Al-Soud ◽  
Søren J. Sørensen ◽  
Niels Kroer
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
Bacterial Community Structure ◽  
High Arctic ◽  
16S Rrna Genes ◽  
Rrna Genes

scholarly journals The Effect of a Sublethal Temperature Elevation on the Structure of Bacterial Communities Associated with the CoralPorites compressa

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Jennifer L. Salerno ◽  
Dan R. Reineman ◽  
Ruth D. Gates ◽  
Michael S. Rappé
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Significant Shift ◽  
Coral Host ◽  
Experimental Conditions

Evidence points to a link between environmental stressors, coral-associated bacteria, and coral disease; however, few studies have examined the details of this relationship under tightly controlled experimental conditions. To address this gap, an array of closed-system, precision-controlled experimental aquaria were used to investigate the effects of an abrupt 1°C above summer ambient temperature increase on the bacterial community structure and photophysiology ofPorites compressacorals. While the temperature treatment rapidly impacted the photophysiology of the coral host, it did not elicit a statistically significant shift in bacterial community structure from control, untreated corals as determined by terminal restriction fragment length polymorphism analysis of 16S rRNA genes. Two of three coral colonies harbored more closely related bacterial communities at the time of collection and, despite statistically significant shifts in bacterial community structure for both control and treatment corals during the 10-day acclimation period, maintained this relationship over the course of the experiment. The experimental design used in this study proved to be a robust, reproducible system for investigating coral microbiology in an aquarium setting.

scholarly journals Axial Dynamics, Stability, and Interspecies Similarity of Bacterial Community Structure in the Highly Compartmentalized Gut of Soil-Feeding Termites (Cubitermes spp.)

2003 ◽  
Vol 69 (10) ◽  
pp. 6018-6024 ◽  
Author(s):  
Dirk Schmitt-Wagner ◽  
Michael W. Friedrich ◽  
Bianca Wagner ◽  
Andreas Brune
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Rflp Analysis ◽  
Companion Paper ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molecular Fingerprints ◽  
Physicochemical Conditions

ABSTRACT The highly compartmentalized gut of soil-feeding termites is characterized by pronounced axial dynamics in physicochemical conditions and microbial processes. In a companion paper (D. Schmitt-Wagner, M. W. Friedrich, B. Wagner, and A. Brune, Appl. Environ. Microbiol. 69:6007-6017, 2003), we demonstrated that the variety of physicochemical conditions in the different gut compartments of Cubitermes spp. is reflected in the diversity of the respective intestinal microbial communities. Here, we used molecular fingerprints of 16S rRNA genes of the bacterial community, obtained by terminal restriction fragment length polymorphism (T-RFLP) analysis, to describe the axial dynamics of the bacterial community structure in the different gut sections. Comparison of the T-RFLP profiles with the predicted terminal restriction fragments of the clones in clone libraries of the gut segments in Cubitermes orthognathus confirmed that all hindgut sections harbored distinct bacterial communities. Morisita indices of community similarity, calculated by comparing the different patterns, revealed large differences between the bacterial communities of soil, gut, and nest material and also among the individual gut sections. By contrast, comparison of the homologous gut segments of different Cubitermes species indicated that the three termite species investigated possessed a similar, gut-specific microbiota that remained comparatively stable even during several months of maintenance in the laboratory.

scholarly journals Stratification of Activity and Bacterial Community Structure in Biofilms Grown on Membranes Transferring Oxygen

2004 ◽  
Vol 70 (4) ◽  
pp. 1982-1989 ◽  
Author(s):  
Alina C. Cole ◽  
Michael J. Semmens ◽  
Timothy M. LaPara
Keyword(s):  
Community Structure ◽  
Organic Carbon ◽  
Bacterial Community ◽  
Flow Velocity ◽  
Bacterial Community Structure ◽  
Respiratory Activity ◽  
Denitrifying Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Biomass Density

ABSTRACT Previous studies have shown that membrane-aerated biofilm (MAB) reactors can simultaneously remove carbonaceous and nitrogenous pollutants from wastewater in a single reactor. Oxygen is provided to MABs through gas-permeable membranes such that the region nearest the membrane is rich in oxygen but low in organic carbon, whereas the outer region of the biofilm is void of oxygen but rich in organic carbon. In this study, MABs were grown under similar conditions but at two different fluid velocities (2 and 14 cm s−1) across the biofilm. MABs were analyzed for changes in biomass density, respiratory activity, and bacterial community structure as functions of biofilm depth. Biomass density was generally highest near the membrane and declined with distance from the membrane. Respiratory activity exhibited a hump-shaped profile, with the highest activity occurring in the middle of the biofilm. Community analysis by PCR cloning and PCR-denaturing gradient gel electrophoresis of 16S rRNA genes demonstrated substantial stratification of the community structure across the biofilm. Population profiles were also generated by competitive quantitative PCR of gene fragments specific for ammonia-oxidizing bacteria (AOB) (amoA) and denitrifying bacteria (nirK and nirS). At a flow velocity of 14 cm s−1, AOB were found only near the membrane, whereas denitrifying bacteria proliferated in the anoxic outer regions of the biofilm. In contrast, at a flow velocity of 2 cm s−1, AOB were either not detected or detected at a concentration near the detection limit. This study suggests that, under the appropriate conditions, both AOB and denitrifying bacteria can coexist within an MAB.

Effects of remediation on the bacterial community of an acid mine drainage impacted stream

2012 ◽  
Vol 58 (11) ◽  
pp. 1316-1326 ◽  
Author(s):  
Suchismita Ghosh ◽  
Moumita Moitra ◽  
Christopher J. Woolverton ◽  
Laura G. Leff
Keyword(s):  
Community Structure ◽  
Acid Mine Drainage ◽  
Bacterial Community ◽  
Environmental Conditions ◽  
Bacterial Community Structure ◽  
Mine Drainage ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Acid Mine ◽  
Reference Stream

Acid mine drainage (AMD) represents a global threat to water resources, and as such, remediation of AMD-impacted streams is a common practice. During this study, we examined bacterial community structure and environmental conditions in a low-order AMD-impacted stream before, during, and after remediation. Bacterial community structure was examined via polymerase chain reaction amplification of 16S rRNA genes followed by denaturing gradient gel electrophoresis. Also, bacterial abundance and physicochemical data (including metal concentrations) were collected and relationships to bacterial community structure were determined using BIO-ENV analysis. Remediation of the study stream altered environmental conditions, including pH and concentrations of some metals, and consequently, the bacterial community changed. However, remediation did not necessarily restore the stream to conditions found in the unimpacted reference stream; for example, bacterial abundances and concentrations of some elements, such as sulfur, magnesium, and manganese, were different in the remediated stream than in the reference stream. BIO-ENV analysis revealed that changes in pH and iron concentration, associated with remediation, primarily explained temporal alterations in bacterial community structure. Although the sites sampled in the remediated stream were in relatively close proximity to each other, spatial variation in community composition suggests that differences in local environmental conditions may have large impacts on the microbial assemblage.

scholarly journals Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation Treatments

2009 ◽  
Vol 75 (19) ◽  
pp. 6258-6267 ◽  
Author(s):  
Etienne Yergeau ◽  
Mélanie Arbour ◽  
Roland Brousseau ◽  
David Juck ◽  
John R. Lawrence ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
High Arctic ◽  
Soil Microbiology ◽  
Ex Situ ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Pcr Targeting

ABSTRACT High-Arctic soils have low nutrient availability, low moisture content, and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at the Canadian high-Arctic stations of Alert (ex situ approach) and Eureka (in situ approach). Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as quantitative reverse transcriptase PCR targeting key functional genes. The results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon-ring-hydroxylating dioxygenases were observed 1 month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e., ex situ versus in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation.

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