scholarly journals Bacterial communities of cryoconite holes of a temperate alpine glacier show both seasonal trends and year-to-year variability

2018 ◽  
Vol 59 (77) ◽  
pp. 1-9 ◽  
Author(s):  
Francesca Pittino ◽  
Maurizio Maglio ◽  
Isabella Gandolfi ◽  
Roberto Sergio Azzoni ◽  
Guglielmina Diolaiuti ◽  
...  
Keyword(s):  
Hot Spots ◽  
Bacterial Communities ◽  
Biological Activities ◽  
Meteorological Data ◽  
Rrna Gene ◽  
Ecological Communities ◽  
Italian Alps ◽  
Glacier Surface ◽  
Alpine Glacier ◽  
Cryoconite Hole

ABSTRACTCryoconite holes are small depressions of the glacier surface filled with melting water and with a wind-blown debris on the bottom. These environments are considered hot spots of biodiversity and biological activities on glaciers and host communities dominated by bacteria. Most of the studies on cryoconite holes assume that their communities are stable. However, evidence of seasonal variation in cryoconite hole ecological communities exists. We investigated the variation of the bacterial communities of cryoconite holes of Forni Glacier (Central Italian Alps) during the melting seasons (July–September) 2013 and 2016, for which samples at three and five time-points, respectively were available. Bacterial communities were characterized by high-throughput Illumina sequencing of the hypervariable V5−V6 regions of 16S rRNA gene, while meteorological data were obtained by an automatic weather station. We found consistent trends in bacterial communities, which shifted from cyanobacteria-dominated communities in July to communities dominated by heterotrophic orders in late August and September. Temperature seems also to affect seasonal dynamics of communities. We also compared bacterial communities at the beginning of the melting season across 4 years (2012, 2013, 2015 and 2016) and found significant year-to-year variability. Cryoconite hole communities on temperate glaciers are therefore not temporally stable.

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 A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1658
Author(s):  
Jan C. Plaizier ◽  
Anne-Mette Danscher ◽  
Paula A. Azevedo ◽  
Hooman Derakhshani ◽  
Pia H. Andersen ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Dry Matter ◽  
Control Diet ◽  
Rrna Gene ◽  
Ruminal Acidosis ◽  
Clustering Patterns ◽  
The 16S Rrna Gene ◽  
Distal Jejunum

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

LWT ◽  
2021 ◽  
Vol 147 ◽  
pp. 111579
Author(s):  
Creciana M. Endres ◽  
Ícaro Maia S. Castro ◽  
Laura D. Trevisol ◽  
Juliana M. Severo ◽  
Michele B. Mann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Bacterial Communities ◽  
Rrna Gene

scholarly journals Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Sonia Ciccazzo ◽  
Alfonso Esposito ◽  
Eleonora Rolli ◽  
Stefan Zerbe ◽  
Daniele Daffonchio ◽  
...  
Keyword(s):  
High Altitude ◽  
Developmental Stage ◽  
Bacterial Communities ◽  
Developmental Stages ◽  
Gene Diversity ◽  
Intergenic Spacer ◽  
Intermediate Stage ◽  
Plant Colonization ◽  
Early Developmental Stage ◽  
Rrna Gene

The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05) on 16S rRNA gene diversity revealed significant differences (P<0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

The structure and diversity of microbiomes of glacial cryoconites (North Caucasus Region)

2021 ◽  
Author(s):  
Ekaterina Ivanova ◽  
Grigory Gladkov ◽  
Anastasiia Kimeklis ◽  
Arina Kichko ◽  
Evgeny Andronov ◽  
...  
Keyword(s):  
Microbial Biomass ◽  
Microbial Consortia ◽  
Biogenic Elements ◽  
Biomass Estimation ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
North Caucasus ◽  
Vegetative Cover ◽  
Glacier Surface ◽  
Amino Acid Synthesis

&lt;p&gt;Studying the diversity and abundance of cryoconite biota is relevant due to global climate warming, since organo-mineral particles in their composition have a significant impact on the ice albedo decrease and, thus, increase the rate of glacier melting. Since cryoconites are &quot;hot spots&quot; for biota development and the only loci where soil-like bodies can form on glaciers, they contribute significantly to the cycles of biogenic elements of ice and oligotrophic ecosystems.&lt;/p&gt;&lt;p&gt;Samples were collected from cryoconites from the Garabashi (GBg_c) and Shkhelda (SHKg_c) glaciers as well as from moraine (Garabashi); nearby soils (Chernozem, Forest-meadow, and organo-accumulative soil) were used as controls.&lt;/p&gt;&lt;p&gt;GBg_c samples were characterized by potentially higher values of microbial biomass (abundance of 16 S rRNA gene copies and ITS), with maximal values in samples taken from the cracked glacier. In contrast, minimal abundance values of the studied taxonomic markers in SHKg_c were determined. The values for the samples of nearby soils occupied an intermediate position. These results may be partially explained by different colors of cryoconites, determined by differences in their biochemical composition and origin: the GBg_c were represented by &quot;black dust&quot;, with low values of albedo and, accordingly, higher values of temperature and moisture, apparently, more favorable for microbial activity compared to the &quot;gray&quot; dust of the SHKg_c.&lt;/p&gt;&lt;p&gt;Taxonomic structure analysis revealed a specific pattern of GBg_c samples&amp;#8211; an oligotrophic psychrophilic community with a pronounced cyanobacterial dominance was detected. Despite significant differences between cryoconites and nearby moraine in the presence of major autotrophic representatives (cyanobacteria Tychonema, Phormidesmis), the heterotrophic component is similar and is represented by a very specific set of soil microorganisms of Bacteroides, Shingomonas, Burkholderiales groups, apparently, due to the flushing out of part of the microbiome from the autotrophic microbial consortia of the glacier, explaining, as well, the grouping of these samples in the Bray-Curtis NMDS ordination. No autotrophic microbiota predominance was detected in SHKg_c, these microbiomes were typical for soils without vegetative cover, as well as without biofilms on the surface (Verrucromicrobia, Sphingomonacia, Bacteroides). A low number of phylotypes was detected for the community of the GBg_c and &amp;#1057;hernozem. Moreover, the alpha-diversity indices were inversely proportional to the results of microbial biomass estimation, which can be explained by greater &quot;homogeneity&quot; (and, apparently, narrower functional specialization) of more numerous communities.&lt;/p&gt;&lt;p&gt;The metabolic profile of cryoconites (according to Picrust2) is characterized by the predominance of aerobic metabolic enzymes (cytochrome c) and proteins (amino acid synthesis), indicating a potentially high level of metabolic activity of the cryoconite microbial community. These results can be explained by the reparative needs of microbial cells under the conditions of oxygenic stress and extremely low temperatures. In contrast to the control soils (especially, Chernozem), relatively low levels of the catalytic pathway and carbon exchange were determined for the cryoconites&amp;#8217; metabolic pathways, possibly associated with both low available carbon stocks and supply of the glacier surface, as compared to soils with higher stocks of available forms of mineral nutrition.&lt;/p&gt;&lt;p&gt;The work is supported by RFBR &amp;#160;project No 19-05-50107.&amp;#160;&lt;/p&gt;

Healthcare microenvironments define multidrug-resistant organism persistence

2021 ◽  
pp. 1-7
Author(s):  
Brendan J. Kelly ◽  
Selamawit Bekele ◽  
Sean Loughrey ◽  
Elizabeth Huang ◽  
Pam Tolomeo ◽  
...  
Keyword(s):  
16S Rrna ◽  
Hot Spots ◽  
Multidrug Resistant ◽  
Systematic Sampling ◽  
Resistant Organism ◽  
Rrna Gene ◽  
Environmental Cleaning ◽  
Healthcare Environment ◽  
Clostridioides Difficile ◽  
Modifiable Factors

Abstract Background: Multidrug-resistant organisms (MDROs) colonizing the healthcare environment have been shown to contribute to risk for healthcare-associated infections (HAIs), with adverse effects on patient morbidity and mortality. We sought to determine how bacterial contamination and persistent MDRO colonization of the healthcare environment are related to the position of patients and wastewater sites. Methods: We performed a prospective cohort study, enrolling 51 hospital rooms at the time of admitting a patient with an eligible MDRO in the prior 30 days. We performed systematic sampling and MDRO culture of rooms, as well as 16S rRNA sequencing to define the environmental microbiome in a subset of samples. Results: The probability of detecting resistant gram-negative organisms, including Enterobacterales, Acinetobacter spp, and Pseudomonas spp, increased with distance from the patient. In contrast, Clostridioides difficile and methicillin-resistant Staphylococcus aureus were more likely to be detected close to the patient. Resistant Pseudomonas spp and S. aureus were enriched in these hot spots despite broad deposition of 16S rRNA gene sequences assigned to the same genera, suggesting modifiable factors that permit the persistence of these MDROs. Conclusions: MDRO hot spots can be defined by distance from the patient and from wastewater reservoirs. Evaluating how MDROs are enriched relative to bacterial DNA deposition helps to identify healthcare micro-environments and suggests how targeted environmental cleaning or design approaches could prevent MDRO persistence and reduce infection risk.

scholarly journals Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts

2011 ◽  
Vol 77 (20) ◽  
pp. 7207-7216 ◽  
Author(s):  
Naomi F. Montalvo ◽  
Russell T. Hill
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Sponge Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Associated Bacteria ◽  
Content Type ◽  
Key Species ◽  
Sponge Associated Bacteria

ABSTRACTThe giant barrel spongesXestospongiamutaandXestospongiatestudinariaare ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences fromX.mutaandX.testudinariashowed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the twoXestospongiaspecies, as well as sequences found also in other sponge species and are dominated by three bacterial groups,Chloroflexi,Acidobacteria, andActinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the twoXestospongiaspecies, and also with the genusXestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts.

scholarly journals Geographical variability of bacterial communities of cryoconite holes of Andean glaciers

2021 ◽  
Author(s):  
Francesca Pittino ◽  
Michael Seeger ◽  
Roberto Azzoni ◽  
Roberto Ambrosini ◽  
Andrea Franzetti
Keyword(s):  
Bacterial Communities ◽  
High Elevation ◽  
Glacier Surface ◽  
Organic Matter Production ◽  
The Andes ◽  
Matter Production ◽  
O2 Concentration ◽  
The World ◽  
Water Ph ◽  
Andean Glaciers

AbstractCryoconite holes, ponds full of melting water with a sediment on the bottom, are hotspot of biodiversity of glacier surface. They host a metabolically active bacterial community that is involved in different dynamics concerning glacier ecosystems. Indeed, they are responsible of organic matter production and with other microorganisms establish a real microecosystem. Cryoconite holes have been described in different areas of the world (e.g., Arctic, Antarctic, Alps, Himalaya), and with this study we will provide the first description of bacterial communities of cryoconite holes of the Andes in South America. We collected samples on three high elevation glaciers of the Andes (Iver, Iver East and Morado glaciers) and two Patagonian glaciers located at sea level (Exploradores glacier and Perito Moreno). Results show that the most abundant orders are Burkholderiales, Cytophagales, Sphingobacteriales, Actinomycetales, Pseudomonadales, Rhodospiarillales, Rhizobiales, Sphingomonadales and Bacteroidales, which have been reported on glaciers of other areas of the world, Bacterial communities change from one glacier to another and both water pH and O2 concentration affect bacterial communities composition.

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.

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