scholarly journals Distinct soil bacterial patterns along narrow and broad elevational gradients in the grassland of Mt. Tianshan, China

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Rui Li ◽  
Yunhua Liu ◽  
Junhui Cheng ◽  
Nana Xue ◽  
Zongjiu Sun ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Distribution Patterns ◽  
Soil Samples ◽  
Community Diversity ◽  
Mean Annual Temperature ◽  
Elevational Gradients ◽  
Bacterial Phyla ◽  
Bacterial Patterns

AbstractBacteria are essential regulators of soil biogeochemical cycles. While several studies of bacterial elevational patterns have been performed in recent years, the drivers of these patterns remain incompletely understood. To clarify bacterial distribution patterns and diversity across narrow- and broad-scale elevational gradients, we collected soil samples from 22 sites in the grasslands of Mt. Tianshan in China along three elevational transects and the overall elevation transect: (1) 6 sites at elevations of 1047–1587 m, (2) 8 sites at 876–3070 m, and (3) 8 sites at 1602–2110 m. The bacterial community diversity across the overall elevation transects exhibited a hump-like pattern, whereas consistent patterns were not observed in the separate elevational transects. The bacterial community composition at the phylum level differed across the transects and elevation sites. The Actinobacteria was the most abundant phylum overall (41.76%) but showed clear variations in the different transects. Furthermore, heatmap analyses revealed that both pH and mean annual temperature (MAT) were significantly (P < 0.05) correlated with bacterial community composition as well as the dominant bacterial phyla, classes, and genera. These findings provide an inclusive view of bacterial community structures in relation to the environmental factors of the different elevational patterns.

scholarly journals Distinct soil bacterial patterns along narrow– and broad–scale elevational gradients in grassland of the Mt. Tianshan, China

2021 ◽  
Author(s):  
Rui Li ◽  
Jiandong Sheng ◽  
Yunhua Liu ◽  
Junhui Cheng ◽  
Zongjiu Sun ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Distribution Patterns ◽  
Community Diversity ◽  
Elevational Gradients ◽  
Community Patterns ◽  
Hump Pattern ◽  
Bacterial Patterns ◽  
Broad Scale

Abstract Bacteria plays a crucial role in soil biogeochemical cycles, bacterial elevational patterns have been well studies over the past decade, but the elevational pattern and its driver poorly understood. To determine the distribution patterns of bacterial composition and diversity across narrow– and broad–scale elevational gradients, we collected soil samples from 22 sites in the grasslands of Mt. Tianshan along three elevational transects and the whole elevation transect: (1) 6 sites at 1047 m – 1587 m, (2) 8 sites at 876 m – 3070 m, and (3) 8 sites at 1602 m – 2110 m. We found a hump pattern of the bacterial community diversity on the whole elevation transect, while not have observed consistent patterns in separately elevation transect. Bacterial community composition based on phylum differed with transects and elevation sites. Furthermore, heatmap analysis showed that pH and MAT significantly (P < 0.05) correlated with bacterial community composition, dominant bacterial phylum and class significantly influenced soil pH. Therefore, our results suggested that soil property plays the most important role in shaping bacterial community patterns in grassland of Mt. Tianshan.

scholarly journals Rhizobacterial communities of five co-occurring desert halophytes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5508 ◽  
Author(s):  
Yan Li ◽  
Yan Kong ◽  
Dexiong Teng ◽  
Xueni Zhang ◽  
Xuemin He ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Community Diversity ◽  
Species Identity ◽  
Halostachys Caspica ◽  
Lycium Ruthenicum ◽  
Limonium Gmelinii

BackgroundRecently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.MethodsFive halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3–V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.ResultsSignificant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity ofHalostachys caspica,Halocnemum strobilaceumandKalidium foliatumassociated bacterial communities was lower than that ofLimonium gmeliniiandLycium ruthenicumcommunities. Furthermore, the composition of the bacterial communities ofHalostachys caspicaandHalocnemum strobilaceumwas very different from those ofLimonium gmeliniiandLycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.DiscussionHalophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

scholarly journals Dynamic succession of substrate-associated bacterial composition and function duringGanoderma lucidumgrowth

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4975 ◽  
Author(s):  
Bo Zhang ◽  
Lijuan Yan ◽  
Qiang Li ◽  
Jie Zou ◽  
Hao Tan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Community Dynamics ◽  
Bacterial Community Composition ◽  
Growth Stages ◽  
Bacterial Phyla ◽  
Medicinal Fungus ◽  
Bacterial Community Dynamics ◽  
Functional Pathway ◽  
And Function

BackgroundGanoderma lucidum, a valuable medicinal fungus, is widely distributed in China. It grows alongside with a complex microbial ecosystem in the substrate. As sequencing technology advances, it is possible to reveal the composition and functions of substrate-associated bacterial communities.MethodsWe analyzed the bacterial community dynamics in the substrate during the four typical growth stages ofG. lucidumusing next-generation sequencing.ResultsThe physicochemical properties of the substrate (e.g. acidity, moisture, total nitrogen, total phosphorus and total potassium) changed between different growth stages. A total of 598,771 sequences from 12 samples were obtained and assigned to 22 bacterial phyla.ProteobacteriaandFirmicuteswere the dominant phyla. Bacterial community composition and diversity significantly differed between the elongation stage and the other three growth stages. LEfSe analysis revealed a large number of bacterial taxa (e.g.Bacteroidetes,AcidobacteriaandNitrospirae) with significantly higher abundance at the elongation stage. Functional pathway prediction uncovered significant abundance changes of a number of bacterial functional pathways between the elongation stage and other growth stages. At the elongation stage, the abundance of the environmental information processing pathway (mainly membrane transport) decreased, whereas that of the metabolism-related pathways increased.DiscussionThe changes in bacterial community composition, diversity and predicted functions were most likely related to the changes in the moisture and nutrient conditions in the substrate with the growth ofG. lucidum, particularly at the elongation stage. Our findings shed light on theG. lucidum-bacteria-substrate relationships, which should facilitate the industrial cultivation ofG. lucidum.

scholarly journals Establishment of a Sink Gallery to Investigate Growth of Carbapenemase-Producing Klebsiella pneumoniae and Biofilms in P-Traps

2020 ◽  
Vol 41 (S1) ◽  
pp. s219-s220
Author(s):  
Christine Ganim ◽  
Mustafa Mazher ◽  
Erin Breaker
Keyword(s):  
Bacterial Community ◽  
Klebsiella Pneumoniae ◽  
Hand Hygiene ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Community Analysis ◽  
Model System ◽  
Community Diversity ◽  
Water Line ◽  
Municipal Water

Background: Hand-hygiene sink drains in healthcare facilities may provide an environment for the survival and dissemination of various multidrug-resistant organisms (MDROs), including carbapenemase-producing Klebsiella pneumoniae (CPKP). We developed a sink model system to establish and test native drinking water biofilms containing CPKP in the p-traps of hand-hygiene sink drains. Methods: A handwashing sink gallery was designed to consist of 6-wall mounted stainless-steel sink basins connected to the same municipal water line. Each sink’s plumbing included a chrome-plated brass p-trap. Healthcare facility conditions were simulated to include handwashing events with the addition of hand-soap and municipal water 4 per day, and nutritional shake (simulating liquid waste) 1 per day. Resultant biofilms in the p-traps of each sink were harvested after 28 days for community analysis. Microbial community analyses were performed on selected biofilm samples using 16S rRNA sequencing of the V4 hypervariable region of genomic DNA. Another experiment evaluated 28-day p-trap biofilm inoculated with CPKP CAV1016 (10 mL 7.010E 7 CFU/mL) and was assessed over 14 days. Heterotrophic plate counts (HPCs) were determined on R2A medium (7 days of incubation at 25C). CPKP was quantified on mEndo selective medium (48 hours of incubation at 36C). Results: Biofilms developed in all p-traps, but biofilm HPC (5.78 mean log CFU/cm2, range 4.35–7.16) and community diversity (15–20 genera per p-trap) varied with sink position. Community analysis showed similarities in bacterial community composition and diversity between sinks 1 and 2, and between sinks 3, 5 and 6, but with differences between the 2 groups. The most abundant family in sinks 3, 5, and 6 was Erythrobacteriaceae (76%, 78%, and 55% of the total reads, respectively), whereas sinks 1 and 2 were dominated by Sphingomonadaceae (63% and 36%) and Methylobacteriaceae (19% and 55%). Also, 16S sequencing revealed the presence of potential opportunistic pathogens in the biofilms, including reads attributed to Pseudomonas and Acinetobacter. CPKP CAV1016 inoculated into 28-day p-trap biofilms colonized and persisted in all 6 sinks for 12 days after inoculation. Conclusions: Despite all 6 sinks sharing an incoming water line, soap, and carbon and energy source, there was a significant variation in the bacterial community composition observed between the sinks. CPKP can colonize and persist in the p-trap biofilms; however, additional work is needed to achieve a reproducible model system. Once this is achieved, the sink gallery will be used to investigate interventions to mitigate colonization or persistence of CPKP in p-trap biofilms.Funding: NoneDisclosures: None

scholarly journals Bacterial Community Composition and Chromophoric Dissolved Organic Matter Differs with Culture Time of Skeletonema dohrnii

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 150
Author(s):  
Yang Liu ◽  
Jinjun Kan ◽  
Jing Yang ◽  
Md Abu Noman ◽  
Jun Sun
Keyword(s):  
Organic Matter ◽  
Bacterial Community ◽  
Dissolved Organic Matter ◽  
Community Composition ◽  
Relative Abundance ◽  
Bacterial Community Composition ◽  
Algal Growth ◽  
Chromophoric Dissolved Organic Matter ◽  
Bacterial Phyla ◽  
Culture Time

Skeletonema dohrnii is a common red tide microalgae occurring in the coastal waters and throughout the world. The associated heterotrophic or autotrophic bacteria play vital roles in regulating algal growth, production, and physiology. In this study, we investigated the detailed bacterial community structure associated with the growth of S. dohrnii’s using high-throughput sequencing-based on 16S rDNA. Our results demonstrated that Bacteroidetes (48.04%) and Proteobacteria (40.66%) in all samples accounted for the majority of bacterial populations. There was a significant linear regression relationship between the abundance of bacterial phyla and culture time. Notable shifts in bacterial community composition were observed during algal growth: Flavobacteriales accounted for the vast majority of sequences at the order level. Furthermore, the relative abundance of Rhodobacterales was gradually reduced during the whole growth process of S. dohrnii (0–12 days). However, beyond that, the relative abundance of Marinobacter was slowly increasing. It is noteworthy that five fluorophores (Peaks T1, T2, I, M, and A) were detected during the growth stage of S. dohrnii. The characteristic indexes (fluorescence index, humification index, and biological index) of chromophoric dissolved organic matter (CDOM) also varied with the culture time. In addition, the taxa of bacteria had certain effects on CDOM and they were inextricably linked to each other.

scholarly journals From source to filter: changes in bacterial community composition during potable water treatment

2017 ◽  
Vol 63 (6) ◽  
pp. 546-558 ◽  
Author(s):  
Enisa Zanacic ◽  
Dena W. McMartin ◽  
John Stavrinides
Keyword(s):  
Water Treatment ◽  
Surface Water ◽  
Rural Communities ◽  
Bacterial Community ◽  
Community Composition ◽  
Potable Water ◽  
Bacterial Community Composition ◽  
Community Diversity ◽  
Valuable Insight ◽  
Source Water

Rural communities rely on surface water reservoirs for potable water. Effective removal of chemical contaminants and bacterial pathogens from these reservoirs requires an understanding of the bacterial community diversity that is present. In this study, we carried out a 16S rRNA-based profiling approach to describe the bacterial consortia in the raw surface water entering the water treatment plants of 2 rural communities. Our results show that source water is dominated by the Proteobacteria, Bacteroidetes, and Cyanobacteria, with some evidence of seasonal effects altering the predominant groups at each location. A subsequent community analysis of transects of a biological carbon filter in the water treatment plant revealed a significant increase in the proportion of Proteobacteria, Acidobacteria, Planctomycetes, and Nitrospirae relative to raw water. Also, very few enteric coliforms were identified in either the source water or within the filter, although Mycobacterium was of high abundance and was found throughout the filter along with Aeromonas, Legionella, and Pseudomonas. This study provides valuable insight into bacterial community composition within drinking water treatment facilities, and the importance of implementing appropriate disinfection practices to ensure safe potable water for rural communities.

scholarly journals Effects of precipitation changes on soil bacterial community composition and diversity in the Junggar desert of Xinjiang, China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8433
Author(s):  
Ke Wu ◽  
Wenxuan Xu ◽  
Weikang Yang
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Nitrogen Concentration ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Northern China ◽  
Soil Bacterial Community ◽  
Factors Affecting ◽  
Bacterial Phyla ◽  
Soil Bacterial

Variation in precipitation can markedly affect the structure and function of soil microbial communities, especially in arid areas which are limited by water resources. Therefore, it is critical to understand how soil bacterial community composition and diversity will respond to variation in precipitation. In this study, we examined the soil bacterial community structure and diversity between five precipitation treatments (60% decrease, 30% decrease, control, 30% increase and 60% increase in precipitation) in the same arid site, in the Junggar desert of Xinjiang, northern China. The dominant bacterial phyla, present at similar frequencies in plots with different precipitation levels, were Actinobacteria, Proteobacteria, Bacteroidetes, Acidobacteria and Chloroflexi. The Shannon-Wiener and Chao1 indices of soil bacterial α-diversity were both positively correlated with plant diversity. Our results indicated that (1) extreme drought significantly decreased bacterial abundance and diversity compared with increased precipitation; (2) variation in precipitation did not change the dominant components of the bacterial communities; and (3) soil pH and total nitrogen concentration were the key factors affecting soil bacterial composition in the Junggar desert.

scholarly journals Insights into the structure and role of seed-borne bacteriome during maize germination

2021 ◽  
Author(s):  
Lidiane Figueiredo dos Santos ◽  
Julie Fernandes Souta ◽  
Cleiton de Paula Soares ◽  
Letícia Oliveira da Rocha ◽  
Maria Luiza Carvalho Santos ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Growth Performance ◽  
Community Composition ◽  
Seedling Growth ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Selective Reduction ◽  
Community Diversity ◽  
Initial Growth

Abstract Seed germination events modulate microbial community composition, which ultimately influences seed to seedling growth performance. Here we evaluate the germinated maize (variety SHS 5050) root bacterial community of disinfected seed (DS) and non-disinfected seed (NDS). Using a gnotobiotic system, sodium hypochlorite (1.25%, 30 min) treated seeds showed a reduction of bacterial population size and an apparent increase of bacterial community diversity associated with a significant selective reduction of Burkholderia related sequences. The shift in the bacterial community composition in DS negatively affects germination speed, seedling growth, and reserve mobilization rates compared with NDS. A synthetic bacterial community (syncom) formed by twelve isolates (9 Burkholderia spp.; 2 Bacillus spp. and 1 Staphylococcus sp.) obtained from natural microbiota maize seeds herein were capable of recovering germination and seedling growth when reintroduced in DS. Overall results showed that changes in bacterial community composition and selective reduction of Burkholderia related members dominance interfere with germination events and initial growth of the maize plantlets. By cultivation-dependent and independent approaches, we deciphered seed-maize microbiome structure, bacterial niches location, and bacterial taxa with relevant roles in seedlings growth performance. A causal relationship between seed microbial community succession and germination performance open opportunities in seed technologies to build-up microbial communities to boost plant growth and health.

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.

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