scholarly journals Glacial Ice Age Shapes Microbiome Composition in a Receding Southern European Glacier

2021 ◽  
Vol 12 ◽  
Author(s):  
Eva Garcia-Lopez ◽  
Ana Moreno ◽  
Miguel Bartolomé ◽  
Maria Leunda ◽  
Carlos Sancho ◽  
...  
Keyword(s):  
Roman Empire ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Green Sulfur Bacteria ◽  
Community Diversity ◽  
Ice Age ◽  
Northern Spain ◽  
Glacial Ice ◽  
Bacterial Phyla ◽  
Over Time

Glaciers and their microbiomes are exceptional witnesses of the environmental conditions from remote times. Climate change is threatening mountain glaciers, and especially those found in southern Europe, such as the Monte Perdido Glacier (northern Spain, Central Pyrenees). This study focuses on the reconstruction of the history of microbial communities over time. The microorganisms that inhabit the Monte Perdido Glacier were identified using high-throughput sequencing, and the microbial communities were compared along an altitudinal transect covering most of the preserved ice sequence in the glacier. The results showed that the glacial ice age gradient did shape the diversity of microbial populations, which presented large differences throughout the last 2000 years. Variations in microbial community diversity were influenced by glacial conditions over time (nutrient concentration, chemical composition, and ice age). Some groups were exclusively identified in the oldest samples as the bacterial phyla Fusobacteria and Calditrichaeota, or the eukaryotic class Rhodophyceae. Among groups only found in modern samples, the green sulfur bacteria (phylum Chlorobi) stood out, as well as the bacterial phylum Gemmatimonadetes and the eukaryotic class Tubulinea. A patent impact of human contamination was also observed on the glacier microbiome. The oldest samples, corresponding to the Roman Empire times, were influenced by the beginning of mining exploitation in the Pyrenean area, with the presence of metal-tolerant microorganisms. The most recent samples comprise 600-year-old ancient ice in which current communities are living.

scholarly journals Fine scale diversification of endolithic microbial communities in the hyper-arid Atacama Desert

2017 ◽  
Author(s):  
Victoria Meslier ◽  
Maria Cristina Casero ◽  
Micah Dailey ◽  
Jacek Wierzchos ◽  
Carmen Ascaso ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Water Retention ◽  
High Throughput Sequencing ◽  
Arid Zone ◽  
Global Climate ◽  
Atacama Desert ◽  
Sampling Strategy ◽  
Physical Structure ◽  
Community Diversity ◽  
Fine Scale

ABSTRACTThe expansion of desertification across our planet is accelerating as the result of human activity and global climate change. In hyper-arid deserts, endolithic microbial communities colonize the rocks’ interior as a survival strategy. Yet, the composition of these communities and the drivers promoting their assembly are still poorly understood. Using a sampling strategy that minimized climate regime and biogeography effects, we analyzed the diversity and community composition of endoliths from four different lithic substrates – calcite, gypsum, ignimbrite and granite – collected in the hyper-arid zone of the Atacama Desert, Chile. By combining microscopy, mineralogy, and high throughput sequencing, we found these communities to be highly specific to their lithic substrate, although they were all dominated by the same four main phyla, Cyanobacteria, Actinobacteria, Chloroflexi and Proteobacteria. This finding indicates a fine scale diversification of the microbial reservoir driven by substrate properties. Our data suggest that the overall rock chemistry is not an essential driver of community structure and we propose that the architecture of the rock, i.e. the space available for colonization and its physical structure, linked to water retention capabilities, is ultimately the driver of community diversity and composition at the dry limit of life.Originality-Significance StatementIn this study, we demonstrated that endolithic microbial communities are highly specific to their substrates, suggesting a fine scale diversification of the available microbial reservoir. By using an array of rock substrates from the same climatic region, we established, for the first time, that the architecture of the rock is linked to water retention and is ultimately the driver of community diversity and composition at the dry limit for life.

scholarly journals Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiota analysis

2019 ◽  
Author(s):  
Emilie Lejal ◽  
Agustín Estrada-Peña ◽  
Maud Marsot ◽  
Jean-François Cosson ◽  
Olivier Rué ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Extraction ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Community Diversity ◽  
Analytical Process ◽  
Sequencing Technologies ◽  
And Gender ◽  
The Impact

AbstractBackgroundThe development of high throughput sequencing technologies has substantially improved analysis of bacterial community diversity, composition, and functions. Over the last decade, high throughput sequencing has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g. individual tick samples, these contaminants may represent a large part of the obtained sequences, and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess the proportion of contaminant sequences resulting from these steps. We analyzed the microbiota of individual Ixodes ricinus ticks by including several categories of controls throughout the analytical process: crushing, DNA extraction, and DNA amplification.ResultsControls yielded a significant number of sequences (1,126 to 13,198 mean sequences, depending on the control category). Some operational taxonomic units (OTUs) detected in these controls belong to genera reported in previous tick microbiota studies. In this study, these OTUs accounted for 50.9% of the total number of sequences in our samples, and were considered contaminants. Contamination levels (i.e. the percentage of sequences belonging to OTUs identified as contaminants) varied with tick stage and gender: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rates lower than 20%. Contamination mainly corresponded to OTUs detected in crushing and DNA extraction controls, highlighting the importance of carefully controlling these steps.ConclusionHere, we showed that contaminant OTUs from extraction and amplification steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples.

scholarly journals Diversity and spoilage potential of microbial communities associated with grape sour rot in eastern coastal areas of China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9376
Author(s):  
Huanhuan Gao ◽  
Xiangtian Yin ◽  
Xilong Jiang ◽  
Hongmei Shi ◽  
Yang Yang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Eastern China ◽  
Grape Berry ◽  
Wine Quality ◽  
Bacterial Phyla ◽  
Sour Rot ◽  
Bacteria And Fungi ◽  
Polymicrobial Disease

As a polymicrobial disease, sour rot decreases grape berry yield and wine quality. The diversity of microbial communities in sour rot-affected grapes depends on the cultivation site, but the microbes responsible for this disease in eastern coastal China, has not been reported. To identify the microbes that cause sour grape rot in this important grape-producing region, the diversity and abundance of bacteria and fungi were assessed by metagenomic analysis and cultivation-dependent techniques. A total of 15 bacteria and 10 fungi were isolated from sour rot-affected grapes. High-throughput sequencing of PCR-amplicons generated from diseased grapes revealed 1343 OTUs of bacteria and 1038 OTUs of fungi. Proteobacteria and Firmicutes were dominant phyla among the 19 bacterial phyla identified. Ascomycota was the dominant fungal phylum and the fungi Issatchenkia terricola, Colletotrichum viniferum, Hanseniaspora vineae, Saprochaete gigas, and Candida diversa represented the vast majority ofmicrobial species associated with sour rot-affected grapes. An in vitro spoilage assay confirmed that four of the isolated bacteria strains (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis) and five of the isolated fungi strains (three Aspergillus species, Alternaria tenuissima, and Fusarium proliferatum) spoiled grapes. These microorganisms, which appear responsible for spoiling grapes in eastern China, appear closely related to microbes that cause this plant disease around the world.

Effect of chemical oxygen demand load on the nitrification and microbial communities in activated sludge from an aerobic nitrifying reactor

2020 ◽  
Vol 66 (1) ◽  
pp. 59-70
Author(s):  
Dan Li ◽  
Xihong Liang ◽  
Zhengwei Li ◽  
Yao Jin ◽  
Rongqing Zhou ◽  
...  
Keyword(s):  
Activated Sludge ◽  
Chemical Oxygen Demand ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Oxygen Demand ◽  
Nitrification Rate ◽  
Culture Time ◽  
Degradation Rates ◽  
Significant Difference ◽  
Over Time

In this study, we explored the effect of chemical oxygen demand (COD) load on the nitrification and microbial communities in activated sludge isolated from an aerobic nitrifying tank. The activated sludge was cultured in three different COD groups: L-COD, 200 mg/L; M-COD, 1200 mg/L; H-COD, 4200 mg/L. The results indicated that the COD exerts a negligible effect on the nitrogen removal ability within the first 24 h. However, the nitrification rate decreased with culture time; the ammonium degradation rates were found to be 80.26%, 57.56%, and 43.43% at 72 h in the three COD groups, respectively. These values correspond to decreases of 19.40%, 41.83%, and 51.48%, respectively, in relation to those observed at 24 h. The activated sludge in the different COD groups exhibited similar community compositions after 24 h, as assessed by Illumina high-throughput sequencing, while a significant difference in the relative abundances of some organisms occurred after 48 and 72 h. Proteobacteria was the main phylum, with a relative abundance of >51.45%. The genera Aridibacter, Paracoccus, Nitrospira, and Nitrosomonas were suppressed by COD load over time. This study may contribute to our knowledge about the nitrification ability and microbial communities in activated sludge at different COD load levels.

scholarly journals The effect of flue-curing procedure on the dynamic change of microbial diversity of tobaccos

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Binbin Hu ◽  
Kaiyuan Gu ◽  
Jiangshiqi Gong ◽  
Ke Zhang ◽  
Dan Chen ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Theoretical Basis ◽  
High Throughput Sequencing ◽  
Dynamic Change ◽  
Community Diversity ◽  
Curing Process ◽  
Tobacco Leaves ◽  
Culture Independent ◽  
Curing Procedure

AbstractThe purpose of the study is to explore the effect of flue-curing procedure on the diversity of microbial communities in tobaccos and the dynamic change of compositions of microbial communities in the flue-curing process. It expects to provide a theoretical basis for the application of microbes in tobacco leaves and a theoretical basis and idea for optimization of the flue-curing technologies. By investigating tobacco variety K326, the tests were carried out for comparing the conventional flue-curing procedure and dry-ball temperature set and wet-ball temperature degradation flue-curing procedure. Based on the culture-independent approach and high-throughput sequencing procedure, the relationship between the flue-curing procedure for tobaccos and microbial communities in tobaccos was revealed by measuring the dynamic change of microbial communities. The results indicated that:(1) Relative to surface wiping method, washing method was more suitable for the sampling of microbes on the surface of tobacco leaves; (2) Dry-ball temperature set and wet-ball temperature degradation flue-curing procedure was more favorable for maintaining the microbial diversity of tobaccos; (3) Relative to bacteria of the tobaccos, the succession rule of the fungal communities in tobaccos was relatively steady; (4)Compared with bacterial community diversity, the fungal community diversity presented an obvious negative correlation with temperature and humidity during the flue-curing process. (5) The function of bacterial communities in tobaccos matched with the material transformation law of tobaccos, having a direct correlation on the flue-curing process. In short, Dry-ball temperature set and wet-ball temperature degradation flue-curing procedure can more favorably maintain the microbial diversity of tobaccos; moreover, the function of the tobacco system involved in microbes in tobaccos was closely related to the material transformation law of tobaccos in the flue-curing process. It validated that the bacteria in tobaccos play an important role in the flue-curing process of tobaccos.

scholarly journals Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

2012 ◽  
Vol 78 (21) ◽  
pp. 7527-7537 ◽  
Author(s):  
David R. Andrew ◽  
Robert R. Fitak ◽  
Adrian Munguia-Vega ◽  
Adriana Racolta ◽  
Vincent G. Martinson ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Sonoran Desert ◽  
Abiotic Factors ◽  
Extreme Environments ◽  
Community Diversity ◽  
Rrna Gene ◽  
Content Type ◽  
Bacterial Phyla ◽  
Culture Independent

ABSTRACTHigh-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundantCrenarchaeotaclassThermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phylaProteobacteria,Actinobacteria,Planctomycetes,Firmicutes,Bacteroidetes,Chloroflexi, andAcidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.

scholarly journals Comparison of Microbial Communities in Colorado Potato Beetles (Leptinotarsa decemlineata Say) Collected From Different Sources in China

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanxue Yu ◽  
Yuhan Wang ◽  
Hongwei Li ◽  
Xin Yu ◽  
Wangpeng Shi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Leptinotarsa Decemlineata ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Economic Losses ◽  
Isolated Populations ◽  
Genus Level ◽  
Potato Beetle ◽  
Leptinotarsa Decemlineata Say ◽  
Dominant Bacteria

Microbial communities in insects are related to their geographical sources and contribute to adaptation to the local habitat. The Colorado potato beetle (Leptinotarsa decemlineata) (CPB) is a potato pest that causes serious economic losses in Xinjiang Uygur Autonomous Region (XJ) and Heilongjiang Province (HL), China. The influence of microorganisms in the invasion and dispersal of CPB is unclear. We studied microbial communities of CPB collected from nine geographic sources in China using high throughput sequencing technology. Bacteroidetes, Firmicutes, and Proteobacteria were the most dominant phyla, Clostridia, Bacteroidetes, and γ-Proteobacteria were the most dominant classes, Enterobacterales, Lactobacillales, Clostridiales, and Bacteroidales were the most dominant orders, and Enterobacteriaceae, Streptococcidae, Verrucomicrobiaceae, and Rikenellaceae were the most dominant families. There were significant differences, among sources, in the relative abundance of taxa at the genus level. A total of 383 genera were identified, and the dominant bacteria at the genus level were compared between XJ and HL. Pseudomonas was the unique dominant microorganism in the HL area, and the other four microorganisms (Lelliottia, Enterococcus, Enterobacter, and Lactococcus) were common within the 2 regions. Bacterial community diversity in CPB from Urumqi, Jimunai, and Wenquan was higher than diversity in other regions. T-Distributed Stochastic Neighbor Embedding (tSNE) analysis indicated that order and genus were appropriate taxonomic levels to distinguish geographical sources of CPB. These findings provide insight into the diversity of microorganisms of CPB in the differences among geographically isolated populations.

scholarly journals Loss of a Single Plant Functional Group in Litter Had Marginal Impacts on Microbial Community Diversity and Composition in a Tibet Fir Forest

2021 ◽  
Author(s):  
Qianwei Li ◽  
Lifeng Wang ◽  
Yamei Chen ◽  
Li Guo ◽  
Chengming You ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Driving Forces ◽  
Community Diversity ◽  
Plant Functional Groups ◽  
Plant Residues ◽  
Microbial Composition ◽  
Ecological Processes ◽  
And Function

Abstract Aim The decomposition of plant residues is a fundamental process of soil organic matter accumulation. The loss of plant functional groups (PFGs) could affect this process by producing litter of different qualities in the soil. Microorganisms are one of the indispensable driving forces of ecological processes, but the mechanisms by microbial communities respond to aboveground PFG changes are still unclear, which limits our understanding of biogeochemical cycle changes under PFG loss.Methods We assessed the microbial taxonomic and functional composition of six typical single PFGs (evergreen conifer, evergreen shrubs, deciduous shrub, graminoid, forb and fern), random loss of a single PFG (SPFG) from litter mixtures and total mixture of six PFGs in a Tibetan fir forest by a high-throughput sequencing method.Results The microbial composition and function did not change with loss of a SPFG in litter, and microbial communities were mainly determined by the carbon and nitrogen ratio (C:N), carbon and phosphorus ratio (C:P), N and lignin, and bacterial functional pathways and fungal functional guilds were both determined by N, C:N and C:P ratios. Bacterial diversity was positively related while fungal diversity was negatively related to N and cellulose concentrations.Conclusion We speculated that the difference in initial litter qualities (especially C:N) between different PFGs, rather than a decreased number of PFGs, is a determinant of microbial composition and function. As the loss of PFG does not change litter quality, the microbial community can resist the loss of PFG, which maintains alpine ecosystem carbon and nutrient cycling stability.

scholarly journals Late-Holocene diatom community response to climate driven chemical changes in a small, subarctic lake, Northwest Territories, Canada

The Holocene ◽  
2021 ◽  
pp. 095968362110032
Author(s):  
Paul B Hamilton ◽  
Scott J Hutchinson ◽  
R Timothy Patterson ◽  
Jennifer M Galloway ◽  
Nawaf A Nasser ◽  
...  
Keyword(s):  
Iron Age ◽  
Biological Diversity ◽  
Regional Climate ◽  
Natural Aging ◽  
Community Response ◽  
Warm Period ◽  
Ice Age ◽  
Diatom Assemblages ◽  
Subarctic Lake ◽  
Over Time

The paleolimnological record of diatoms and climate, spanning the last 2800 years, was investigated in a small subarctic lake (Pocket Lake) that from AD 1948 to 2004 was contaminated by gold smelting waste. An age-depth model was constructed using a combination of 210Pb, 14C, and tephra to determine a 2800 year history of lake ontogeny (natural aging), biological diversity, and regional climate variability. Diatoms form six strong paleoecological assemblages over time in response to changes in local hydrological and sedimentological conditions (including metals). Selected environmental variables explained 28.8% of the variance in the diatom assemblages, with Fe, Ca, and sediment end member distribution being important indicators. The diatom assemblages correlated to the Iron Age Cold Epoch (2800–2300 cal BP), Roman Warm Period (2250–1610 cal BP), Dark Age Cold Period (1500–1050 cal BP), Medieval Climate Anomaly (ca. 1100–800 cal BP), and the Little Ice Age (800–200 cal BP). The disappearance of Staurosira venter highlights the change from the Iron Age Cold Epoch to the Roman Warm Period. After deposition of the White River Ash (833–850 CE; 1117–1100 cal BP), transition to circumneutral conditions was followed in tandem by a transition to planktic influenced communities. Ten discrete peaks of Cu, Pb, and Zn were observed and attributed to soluble mobility from catchment soils through enhanced seepage and spring snowmelt. The prominent metal spikes were aligned with increases in Brachysira neoexilis. Downward mobilization of arsenic and antimony from contaminated surficial sediments highlight the problem of post depositional industrial contamination of paleosediments. Results demonstrate that paleoclimatic changes in the region, modulated by solar radiation, impacted temperature and precipitation in the lake catchment, influencing temporal shifts in diatom ecology. Changes in diatom taxa richness provided valuable information on the relative influence of water quality (planktic taxa) and sediment input (benthic taxa). The diatom assemblage succession also provides evidence that natural aging over time has played a role in the ecological evolution of the lake.

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