scholarly journals The Bacterial Community Associated with the Amarillo Zamorano Maize (Zea mays) Landrace Silage Process

2020 ◽  
Vol 8 (10) ◽  
pp. 1503
Author(s):  
Humberto Ramírez-Vega ◽  
Ramón I. Arteaga-Garibay ◽  
Otoniel Maya-Lucas ◽  
Victor M. Gómez-Rodríguez ◽  
Ismael F. Chávez-Díaz ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Rrna Gene ◽  
Local Conditions ◽  
Operational Taxonomic Units ◽  
Maize Seeds ◽  
Hypervariable Regions ◽  
Silage Fermentation ◽  
Silage Process ◽  
Next Generation Sequencing Ngs

Maize silage is used in the diet of dairy cows, with suitable results in milk yield. In this study, the composition and diversity of the bacterial communities of the silage process of Amarillo Zamorano (AZ) Mexican maize landrace with relation to the Antilope (A) commercial hybrid are described. From both types of maize, seeds were sown in experimental plots, plants harvested at the reproductive stage, chopped, and packed in laboratory micro-silos. Physicochemical parameters were evaluated, and DNA was extracted from the juice in the micro-silos. The bacterial communities were analyzed by next-generation sequencing (NGS) of seven hypervariable regions of the 16S rRNA gene. The composition of both bacterial communities was dominated by Lactobacillales and Enterobacteriales, Lactobacillales mainly in A silage and Enterobacteriales in AZ silage; as well, the core bacterial community of both silages comprises 212 operational taxonomic units (OTUs). Sugar concentration showed the highest number of significant associations with OTUs of different phyla. The structure of the bacterial communities was different in both silage fermentation processes, showing that AZ silage has a shorter fermentation process than A silage. In addition, NGS demonstrated the effect of the type of maize and local conditions on silage fermentation and contributed to potential strategies to improve the quality of AZ silage.

scholarly journals Uterine and vaginal bacterial community diversity prior to artificial insemination between pregnant and nonpregnant postpartum cows1

2019 ◽  
Vol 97 (10) ◽  
pp. 4298-4304 ◽  
Author(s):  
Taylor B Ault ◽  
Brooke A Clemmons ◽  
Sydney T Reese ◽  
Felipe G Dantas ◽  
Gessica A Franco ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Artificial Insemination ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Beef Cows ◽  
Community Diversity ◽  
Rrna Gene ◽  
Bacterial Community Diversity ◽  
Hypervariable Regions ◽  
Time Of Breeding

Abstract The present study evaluated the bovine vaginal and uterine bacterial community diversity and its relationship to fertility. Postpartum beef cows (n = 68) were synchronized beginning on day −21 and ending with timed artificial insemination (TAI) on day 0. Pregnancy was diagnosed 30 d after TAI. Uterine and vaginal flushes were collected on day −21, −9, and −2 for bacterial DNA extraction to sequence the V1 to V3 hypervariable regions of the 16S rRNA gene. Results indicated a decrease in the number of bacterial species over time in the uterus of resulting pregnant and nonpregnant beef cows (P < 0.0001). Principal coordinate analyses (PCoA) depicted clustering of samples, indicating closely related bacterial communities, by day in the uterus and vagina (P < 0.0001). At day −2, uterine samples from nonpregnant and pregnant animals clustered separately (P < 0.0001), with nonpregnant animal samples clustering tightly together. Overall, the current study suggests the shift in the reproductive bacterial communities’ diversity and phylogenetic relationship leading up to the time of breeding may contribute to successful pregnancy establishment.

scholarly journals Impact of Virioplankton on Archaeal and Bacterial Community Richness as Assessed in Seawater Batch Cultures

2004 ◽  
Vol 70 (2) ◽  
pp. 804-813 ◽  
Author(s):  
Christian Winter ◽  
Arjan Smit ◽  
Gerhard J. Herndl ◽  
Markus G. Weinbauer
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Tropical Atlantic ◽  
Viral Lysis ◽  
Batch Cultures ◽  
Operational Taxonomic Units ◽  
The Impact

ABSTRACT During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.

scholarly journals Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau

2019 ◽  
Author(s):  
Luciano Lopes Queiroz ◽  
Amanda Gonçalves Bendia ◽  
Rubens Tadeu Delgado Duarte ◽  
Diego Assis das Graças ◽  
Artur Luiz da Costa da Silva ◽  
...  
Keyword(s):  
Deep Sea ◽  
Bacterial Communities ◽  
Sao Paulo ◽  
Rrna Gene ◽  
São Paulo ◽  
Operational Taxonomic Units ◽  
Uncultured Bacteria ◽  
Abundant Otus ◽  
Sediment Layers ◽  
Next Generation Sequencing Ngs

AbstractHere we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing (NGS) method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2,456-2,728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaprotebacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.

scholarly journals The capacity of wastewater treatment plants drives bacterial community structure and its assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Young Kyung Kim ◽  
Keunje Yoo ◽  
Min Sung Kim ◽  
Il Han ◽  
Minjoo Lee ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Activated Sludge ◽  
Community Assembly ◽  
Bacterial Communities ◽  
Wastewater Treatment Plants ◽  
High Capacity ◽  
Operating Conditions ◽  
Rrna Gene

Abstract Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

scholarly journals Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

2021 ◽  
Vol 12 ◽  
Author(s):  
Larissa Frühe ◽  
Verena Dully ◽  
Dominik Forster ◽  
Nigel B. Keeley ◽  
Olivier Laroche ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Environmental Dna ◽  
Community Diversity ◽  
Rrna Gene ◽  
Local Conditions ◽  
Global Trends ◽  
Bacterial Taxon ◽  
Metabolic Properties

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3–V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

scholarly journals Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding

2020 ◽  
Vol 11 ◽  
Author(s):  
Pasquale Alibrandi ◽  
Sylvia Schnell ◽  
Silvia Perotto ◽  
Massimiliano Cardinale
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Host Plant ◽  
Bacterial Communities ◽  
Reproductive Organs ◽  
Distribution Model ◽  
Rrna Gene ◽  
Orchid Species ◽  
Core Microbiota

The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.

scholarly journals Ecological Succession of Bacterial Communities during Conventionalization of Germ-Free Mice

2012 ◽  
Vol 78 (7) ◽  
pp. 2359-2366 ◽  
Author(s):  
Merritt G. Gillilland ◽  
John R. Erb-Downward ◽  
Christine M. Bassis ◽  
Michael C. Shen ◽  
Galen B. Toews ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Bacterial Communities ◽  
Structural Heterogeneity ◽  
Ecological Succession ◽  
Rrna Gene ◽  
Gi Tract ◽  
Content Type ◽  
Germ Free ◽  
Over Time

ABSTRACTLittle is known about the dynamics of early ecological succession during experimental conventionalization of the gastrointestinal (GI) tract; thus, we measured changes in bacterial communities over time, at two different mucosal sites (cecum and jejunum), with germfree C57BL/6 mice as the recipients of cecal contents (input community) from a C57BL/6 donor mouse. Bacterial communities were monitored using pyrosequencing of 16S rRNA gene amplicon libraries from the cecum and jejunum and analyzed by a variety of ecological metrics. Bacterial communities, at day 1 postconventionalization, in the cecum and jejunum had lower diversity and were distinct from the input community (dominated by eitherEscherichiaorBacteroides). However, by days 7 and 21, the recipient communities had become significantly diverse and the cecal communities resembled those of the donor and donor littermates, confirming that transfer of cecal contents results in reassembly of the community in the cecum 7 to 21 days later. However, bacterial communities in the recipient jejunum displayed significant structural heterogeneity compared to each other or the donor inoculum or the donor littermates, suggesting that the bacterial community of the jejunum is more dynamic during the first 21 days of conventionalization. This report demonstrates that (i) mature input communities do not simply reassemble at mucosal sites during conventionalization (they first transform into a “pioneering” community and over time take on the appearance, in membership and structure, of the original input community) and (ii) the specific mucosal environment plays a role in shaping the community.

scholarly journals The Wheat Microbiome Under Four Management Strategies, and Potential for Endophytes in Disease Protection

2017 ◽  
Vol 1 (3) ◽  
pp. 158-168 ◽  
Author(s):  
Kristi Gdanetz ◽  
Frances Trail
Keyword(s):  
Bacterial Communities ◽  
Management Strategy ◽  
Crop Yields ◽  
Management Strategies ◽  
Growing Season ◽  
Amplicon Sequencing ◽  
Antagonistic Activity ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Plant Organ

Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different crop management strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy.

Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish

2019 ◽  
Author(s):  
Lara Parata ◽  
Shaun Nielsen ◽  
Xing Xing ◽  
Torsten Thomas ◽  
Suhelen Egan ◽  
...  
Keyword(s):  
Coral Reef ◽  
Gastrointestinal Tract ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Food Source ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Symbionts ◽  
Adult Fish

Abstract Herbivorous fishes play important ecological roles in coral reefs by consuming algae that can otherwise outcompete corals, but we know little about the gut microbiota that facilitates this process. This study focussed on the gut microbiota of an ecologically important coral reef fish, the convict surgeonfish Acanthurus triostegus. We sought to understand how the microbiome of this species varies along its gastrointestinal tract and how it varies between juvenile and adult fish. Further, we examined if the bacteria associated with the diet consumed by juveniles contributes to the gut microbiota. 16S rRNA gene amplicon sequencing showed that bacterial communities associated with the midgut and hindgut regions were distinct between adults and juveniles, however, no significant differences were seen for gut wall samples. The microbiota associated with the epilithic algal food source was similar to that of the juvenile midgut and gut wall but differed from the microbiome of the hindgut. A core bacterial community including members of taxa Epulopiscium and Brevinemataceae was observed across all gastrointestinal and diet samples, suggesting that these bacterial symbionts can be acquired by juvenile convict surgeonfish horizontally via their diet and then are retained into adulthood.

Bacteria in tropical floodplain soils are sensitive to changes in saltwater

2018 ◽  
Vol 69 (7) ◽  
pp. 1110 ◽  
Author(s):  
Tiffanie M. Nelson ◽  
Claire Streten ◽  
Karen S. Gibb ◽  
Anthony A. Chariton
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Saltwater Intrusion ◽  
National Park ◽  
Wetland Soils ◽  
Rrna Gene ◽  
Northern Australia ◽  
Tropical River ◽  
16S Rrna Gene Pyrosequencing ◽  
Freshwater Habitats

Bacterial communities in floodplain and wetland soils cycle elements essential for flora and fauna. The coastal habitats of northern Australia are threatened with increasing saltwater intrusion (SWI) events that will destroy freshwater habitats. The effect of the impending SWI on bacterial communities is unknown. Here, we examined the bacterial communities of a tropical river floodplain located in World Heritage Kakadu National Park. Using 16S rRNA gene pyrosequencing, we measured the baseline bacterial communities from three morphologically distinct regions of the floodplain (lower, upper and backwater swamp), within three zones of the South Alligator River (upstream, cuspate and estuarine funnel or sinuous). Significant differences in the bacterial community were observed at each category of floodplain morphology and river zone. The greatest differences were due to pH and salinity. Large changes in bacterial compositions are predicted to occur with increases in salinity and pH. Saltwater intrusion is predicted to increase substantially in the next decades with sea-level rise, and is likely to cause large and significant changes to the bacterial community with unknown consequences for biogeochemical cycling. Kakadu National Park may benefit from incorporating bacteria into routine studies, because we have shown here that they are sensitive indicators of change, even across small ranges of abiotic variables.

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