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 Microbial colonization of chasmoendolithic habitats in the hyper-arid zone of the Atacama Desert

2012 ◽  
Vol 9 (11) ◽  
pp. 15603-15632
Author(s):  
J. DiRuggiero ◽  
J. Wierzchos ◽  
C. K. Robinson ◽  
T. Souterre ◽  
J. Ravel ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Heterotrophic Bacteria ◽  
Arid Zone ◽  
Atacama Desert ◽  
Community Diversity ◽  
Microbial Colonization ◽  
Climate Data ◽  
Microbial Life ◽  
Total Community ◽  
Diverse Community

Abstract. Efforts in searching for microbial life in the driest part of Atacama Desert, Chile, revealed a small number of lithic habitats that can be considered as environmental refuges for life. In this study, we describe for the first time chasmoendolithic colonization of fissures and cracks of rhyolite-gypsum and calcite rocks collected in the hyper-arid zone of the desert. The use of high-throughput sequencing revealed that the Atacama rock communities comprised a few dominant phylotypes and a number of less abundant taxa representing the majority of the total community diversity. The chasmoendolithic communities were dominated by Chroococcidiopsis species cyanobacteria and supported a number of novel heterotrophic bacteria. Micro-climate data and geomorphic analysis of the mineral substrates suggested higher water availability in the calcite rocks in the form of enhanced water retention in the complex network of cracks and fissures of these rocks as well as increased occurrence of liquid water in the form of dewfall. These characteristics were associated with a diverse community of phototrophic and heterotrophic bacteria in the calcite chasmoendolithic ecosystem. This study is another example of the diversity of adaptive strategies at the limit for life and illustrates that rock colonization is controlled by a complex set of factors.

scholarly journals Microbial colonisation of chasmoendolithic habitats in the hyper-arid zone of the Atacama Desert

2013 ◽  
Vol 10 (4) ◽  
pp. 2439-2450 ◽  
Author(s):  
J. DiRuggiero ◽  
J. Wierzchos ◽  
C. K. Robinson ◽  
T. Souterre ◽  
J. Ravel ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Heterotrophic Bacteria ◽  
Arid Zone ◽  
Atacama Desert ◽  
Community Diversity ◽  
Climate Data ◽  
Microbial Life ◽  
Total Community ◽  
Diverse Community ◽  
First Time

Abstract. Efforts in searching for microbial life in the driest part of Atacama Desert, Chile, revealed a small number of lithic habitats that can be considered as environmental refuges for life. In this study, we describe for the first time chasmoendolithic colonisation of fissures and cracks of rhyolite-gypsum and calcite rocks collected in the hyper-arid zone of the desert. The use of high-throughput sequencing revealed that the Atacama rock communities comprised a few dominant phylotypes and a number of less abundant taxa representing the majority of the total community diversity. The chasmoendolithic communities were dominated by Chroococcidiopsis species cyanobacteria and supported a number of heterotrophic bacterial lineages. Micro-climate data and geomorphic analysis of the mineral substrates suggested higher water availability in the calcite rocks in the form of enhanced water retention in the complex network of cracks and fissures of these rocks as well as increased occurrence of liquid water in the form of dewfall. These characteristics were associated with a diverse community of phototrophic and heterotrophic bacteria in the calcite chasmoendolithic ecosystem. This study is another example of the diversity of adaptive strategies at the limit for life and illustrates that rock colonisation is controlled by a complex set of factors.

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 The composition of endolithic communities in gypcrete is determined by the specific microhabitat architecture

2020 ◽  
Author(s):  
María Cristina Casero ◽  
Victoria Meslier ◽  
Jocelyne DiRuggiero ◽  
Antonio Quesada ◽  
Carmen Ascaso ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Environmental Conditions ◽  
High Throughput Sequencing ◽  
Atacama Desert ◽  
Bottom Layer ◽  
Essential Factor ◽  
Microscopy Techniques ◽  
First Time ◽  
Endolithic Communities

Abstract. Endolithic microhabitats have been described as the last refuge for life in arid and hyper-arid deserts where life has to deal with harsh environmental conditions. A number of rock substrates from the hyper-arid Atacama Desert, colonized by endolithic microbial communities, such as halite, gypsum crusts, gypcrete, calcite, granite and ignimbrite, have been characterized and compared using different approaches. In this work, three different endolithic microhabitats are described, each one with a particular origin and architecture, found within a lithic substrate known as gypcrete. Gypcrete, an evaporitic rock mainly composed of gypsum (CaSO4 ⋅ 2H2O) and collected in the Cordón de Lila area of the desert (Preandean Atacama Desert), was found to harbour cryptoendolithic (within pore spaces in the rock), chasmoendolithic (within cracks and fissures) and hypoendolithic (within microcave-like pores in rock-bottom layer) microhabitats. A combination of microscopy investigations strategies and high-throughput sequencing approaches were used to characterize the endolithic communities at the microscale in these microhabitats within the same piece of lithic substrate. Microscopy techniques revealed differences in the architecture of the endolithic microhabitats and in the distribution of the microorganisms within those microhabitats. Cyanobacteria and Proteobacteria were dominant in the endolithic communities, of which the hypoendolithic community was the least diverse and hosted unique taxa. These results show, for the first time, that the differences in the architecture of a microhabitat, even within the same piece of lithic substrate, might be an essential factor in shaping the diversity and composition of endolithic microbial communities.

scholarly journals The composition of endolithic communities in gypcrete is determined by the specific microhabitat architecture

2021 ◽  
Vol 18 (3) ◽  
pp. 993-1007
Author(s):  
María Cristina Casero ◽  
Victoria Meslier ◽  
Jocelyne DiRuggiero ◽  
Antonio Quesada ◽  
Carmen Ascaso ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Essential Role ◽  
High Throughput Sequencing ◽  
Atacama Desert ◽  
Bottom Layer ◽  
Microscopy Investigation ◽  
Microscopy Techniques ◽  
First Time ◽  
Endolithic Communities

Abstract. Endolithic microhabitats have been described as the last refuge for life in arid and hyper-arid deserts where life has to deal with harsh environmental conditions. A number of rock substrates from the hyper-arid Atacama Desert, colonized by endolithic microbial communities such as halite, gypsum crusts, gypcrete, calcite, granite and ignimbrite, have been characterized and compared using different approaches. In this work, three different endolithic microhabitats are described, each one with a particular origin and architecture, found within a lithic substrate known as gypcrete. Gypcrete, an evaporitic rock mainly composed of gypsum (CaSO4 ⋅ 2H2O) and collected in the Cordón de Lila area of the desert (Preandean Atacama Desert), was found to harbour cryptoendolithic (within pore spaces in the rock), chasmoendolithic (within cracks and fissures) and hypoendolithic (within microcave-like pores in the bottom layer of rock) microhabitats. A combination of microscopy investigation and high-throughput sequencing approaches were used to characterize the endolithic communities and their habitats at the microscale within the same piece of gypcrete. Microscopy techniques revealed differences in the architecture of the endolithic microhabitats and the distribution of the microorganisms within those microhabitats. Cyanobacteria and Proteobacteria were dominant in the endolithic communities, of which the hypoendolithic community was the least diverse and hosted unique taxa, as a result of less access to sun radiation. These results show, for the first time, that the differences in the architecture of a microhabitat, even within the same piece of a lithic substrate, play an essential role in shaping the diversity and composition of endolithic microbial communities.

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 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 Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology

Environments ◽  
2021 ◽  
Vol 8 (2) ◽  
pp. 16
Author(s):  
Sergey Kharitonov ◽  
Mikhail Semenov ◽  
Alexander Sabrekov ◽  
Oleg Kotsyurbenko ◽  
Alena Zhelezova ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Global Climate ◽  
Methane Flux ◽  
Molecular Methods ◽  
Methane Cycle ◽  
Selective Enrichment ◽  
Global Climate Changes ◽  
Wide Range

The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identification techniques, such as selective enrichment and pure-culture isolation, have been used for a long time to study diversity of methanogens and methanotrophs. However, these techniques are characterized by significant limitations, since only a relatively small fraction of the microbial community could be cultured. Modern molecular methods for quantitative analysis of the microbial community such as real-time PCR (Polymerase chain reaction), DNA fingerprints and methods based on high-throughput sequencing together with different “omics” techniques overcome the limitations imposed by culture-dependent approaches and provide new insights into the diversity and ecology of microbial communities in the methane cycle. Here, we review available knowledge concerning the abundances, composition, and activity of methanogenic and methanotrophic communities in a wide range of natural and anthropogenic environments. We suggest that incorporation of microbial data could fill the existing microbiological gaps in methane flux modeling, and significantly increase the predictive power of models for different environments.

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 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.

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