scholarly journals Experimental and molecular approximation to microbial niche: trophic interactions between oribatid mites and microfungi in an oligotrophic freshwater system

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5200 ◽  
Author(s):  
Patricia Velez ◽  
Margarita Ojeda ◽  
Laura Espinosa-Asuar ◽  
Tila M. Pérez ◽  
Luis E. Eguiarte ◽  
...  
Keyword(s):  
Nutrient Dynamics ◽  
Chihuahuan Desert ◽  
Extreme Environments ◽  
Genetic Lineage ◽  
Direct Pcr ◽  
Culture Independent ◽  
Freshwater System ◽  
Cuatro Ciénegas Basin ◽  
Fungal Interactions

Mite-fungal interactions play a key role in structuring core ecosystem processes such as nutrient dynamics. Despite their ecological relevance, these cross-kingdom interactions remain poorly understood particularly in extreme environments. Herein, we investigated feeding preferences of a novel genetic lineage of aquatic oribatids obtained from an oligotrophic freshwater system in the Cuatro Ciénegas Basin (CCB) within the Chihuahuan Desert, Mexico. During in vitro diet preference bioassays, transient aquatic microfungi (Aspergillus niger, Talaromyces sp., and Pleosporales sp.) recovered from the same mesocosm samples were offered individually and simultaneously to mites. Gut content was analyzed using classic plating and culture-independent direct PCR (focusing on the fungal barcoding region) methods. Our results indicated that oribatids fed on all tested fungal isolates, yet the profusely developing A. niger was preferentially consumed with all fungal components being digested. This feeding habit is particularly interesting since A. niger has been reported as an unsuitable dietary element for population growth, being consistently avoided by mites in previous laboratory experiments. It is possible that our mites from the CCB have adapted to exploit available resources within this oligotrophic site. This work confirms the trophic relationship between microfungi and mites, two rarely investigated major components of the microbial community, shedding light on the niche dynamics under low-nutrient conditions.

scholarly journals High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

2017 ◽  
Author(s):  
Hector Fernando Arocha-Garza ◽  
Ricardo Canales-Del Castillo ◽  
Luis E. Eguiarte ◽  
Valeria Souza ◽  
Susana De la Torre-Zavala
Keyword(s):  
16S Rdna ◽  
Chihuahuan Desert ◽  
Extreme Environments ◽  
Sampling Period ◽  
Dispersal Limitation ◽  
Small Scale ◽  
Rarefaction Analysis ◽  
Biogeographic Patterns ◽  
Evolutionary Context ◽  
Cuatro Ciénegas Basin

The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media. The 16S rDNA of putative Actinobacteria were sequenced using both bacteria universal and phylum-specific primer pairs. Phylogenetic reconstructions were performed to analyze OTUs clustering and taxonomic identification of the isolates in an evolutionary context, using validated type species of Streptomyces from previously phylogenies as a reference. Rarefaction analysis for total Actinobacteria and for Streptomyces isolates were performed to estimate species´ richness in the intermediate lagoon (IL) in the oligotrophic Churince system. A total of 350 morphologically and nutritionally diverse isolates were successfully cultured and characterized as members of the Phylum Actinobacteria. 105 from the total isolates were successfully subcultured, processed for DNA extraction and 16S-rDNA sequenced. All strains belong to the order Actinomycetales, encompassing 11 genera of Actinobacteria; the genus Streptomyces was found to be the most abundant taxa in all the media tested throughout the 3-year sampling period. Phylogenetic analysis of our isolates and another 667 reference strains of the family Streptomycetaceae shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

scholarly journals Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth's history

2021 ◽  
Author(s):  
David Madrigal-Trejo ◽  
Jazmín Sánchez-Pérez ◽  
Laura Espinosa-Asuar ◽  
Valeria Souza
Keyword(s):  
Fossil Record ◽  
Microbial Mats ◽  
Chihuahuan Desert ◽  
Extreme Environments ◽  
Taxonomic Composition ◽  
Ecological Stability ◽  
The Face ◽  
Microbial System ◽  
Cuatro Ciénegas ◽  
Cuatro Ciénegas Basin

Microbial mats are complex ecological assemblages that are found in the Precambrian fossil record and in extant extreme environments. Hence, these structures are regarded as highly stable ecosystems. In this work, we assess the ecological stability in a modern, fluctuating, hypersaline pond from the Cuatro Ciénegas Basin. From the 2016 to 2019 metagenomic sampling of this site, we found that this microbial site is sensitive to disturbances, which leads to high taxonomic replacement. Additionally, the mats have shown to be functionally stable throughout time, and could be differentiated between dry and rainy seasonal states. We speculate that this microbial system could represent a modern analog of ancient, hypersaline coastal microbial mats, where functions were preserved over time, whereas taxonomic composition was subject to diversification in the face of local and planetary perturbations.

scholarly journals High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

2017 ◽  
Author(s):  
Hector Fernando Arocha-Garza ◽  
Ricardo Canales-Del Castillo ◽  
Luis E. Eguiarte ◽  
Valeria Souza ◽  
Susana De la Torre-Zavala
Keyword(s):  
16S Rdna ◽  
Chihuahuan Desert ◽  
Extreme Environments ◽  
Sampling Period ◽  
Dispersal Limitation ◽  
Small Scale ◽  
Rarefaction Analysis ◽  
Biogeographic Patterns ◽  
Evolutionary Context ◽  
Cuatro Ciénegas Basin

The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media. The 16S rDNA of putative Actinobacteria were sequenced using both bacteria universal and phylum-specific primer pairs. Phylogenetic reconstructions were performed to analyze OTUs clustering and taxonomic identification of the isolates in an evolutionary context, using validated type species of Streptomyces from previously phylogenies as a reference. Rarefaction analysis for total Actinobacteria and for Streptomyces isolates were performed to estimate species´ richness in the intermediate lagoon (IL) in the oligotrophic Churince system. A total of 350 morphologically and nutritionally diverse isolates were successfully cultured and characterized as members of the Phylum Actinobacteria. 105 from the total isolates were successfully subcultured, processed for DNA extraction and 16S-rDNA sequenced. All strains belong to the order Actinomycetales, encompassing 11 genera of Actinobacteria; the genus Streptomyces was found to be the most abundant taxa in all the media tested throughout the 3-year sampling period. Phylogenetic analysis of our isolates and another 667 reference strains of the family Streptomycetaceae shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

scholarly journals High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3247 ◽  
Author(s):  
Hector Fernando Arocha-Garza ◽  
Ricardo Canales-Del Castillo ◽  
Luis E. Eguiarte ◽  
Valeria Souza ◽  
Susana De la Torre-Zavala
Keyword(s):  
16S Rdna ◽  
Chihuahuan Desert ◽  
Extreme Environments ◽  
Sampling Period ◽  
Dispersal Limitation ◽  
Small Scale ◽  
Rarefaction Analysis ◽  
Biogeographic Patterns ◽  
Evolutionary Context ◽  
Cuatro Ciénegas Basin

The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media. The 16S rDNA of putative Actinobacteria were sequenced using both bacteria universal and phylum-specific primer pairs. Phylogenetic reconstructions were performed to analyze OTUs clustering and taxonomic identification of the isolates in an evolutionary context, using validated type species ofStreptomycesfrom previously phylogenies as a reference. Rarefaction analysis for total Actinobacteria and for Streptomyces isolates were performed to estimate species’ richness in the intermediate lagoon (IL) in the oligotrophic Churince system. A total of 350 morphologically and nutritionally diverse isolates were successfully cultured and characterized as members of the Phylum Actinobacteria. A total of 105 from the total isolates were successfully subcultured, processed for DNA extraction and 16S-rDNA sequenced. All strains belong to the order Actinomycetales, encompassing 11 genera of Actinobacteria; the genusStreptomyceswas found to be the most abundant taxa in all the media tested throughout the 3-year sampling period. Phylogenetic analysis of our isolates and another 667 reference strains of the family Streptomycetaceae shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

scholarly journals The Diversity of Root-Associated Endophytic Fungi from Four Epiphytic Orchids in China

Diversity ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 197
Author(s):  
Tao Wang ◽  
Miao Chi ◽  
Ling Guo ◽  
Donghuan Liu ◽  
Yu Yang ◽  
...  
Keyword(s):  
Endophytic Fungi ◽  
Southern China ◽  
Culture Method ◽  
Amplicon Sequencing ◽  
Community Diversity ◽  
Mycorrhizal Symbiosis ◽  
Epiphytic Orchids ◽  
Culture Independent ◽  
Almost All

Root-associated endophytic fungi (RAF) are found asymptomatically in almost all plant groups. However, little is known about the compositions and potential functions of RAF communities associated with most Orchidaceae species. In this study, the diversity of RAF was examined in four wild epiphytic orchids, Acampe rigida, Doritis pulcherrima, Renanthera coccinea, and Robiquetia succisa, that occur in southern China. A culture-independent method involving Illumina amplicon sequencing, and an in vitro culture method, were used to identify culturable fungi. The RAF community diversity differed among the orchid roots, and some fungal taxa were clearly concentrated in a certain orchid species, with more OTUs being detected. By investigating mycorrhizal associations, the results showed that 28 (about 0.8%) of the 3527 operational taxonomic units (OTUs) could be assigned as OMF, while the OTUs of non-mycorrhizal fungal were about 99.2%. Among the OMFs, Ceratobasidiaceae OTUs were the most abundant with different richness, followed by Thelephoraceae. In addition, five Ceratobasidium sp. strains were isolated from D. pulcherrima, R. succisa, and R. coccinea roots with high separation rates. These culturable Ceratobasidium strains will provide materials for host orchid conservation and for studying the mechanisms underlying mycorrhizal symbiosis.

scholarly journals Hlf Expression Marks Early Emergence of Hematopoietic Stem Cell Precursors With Adult Repopulating Potential and Fate

2021 ◽  
Vol 9 ◽  
Author(s):  
Wanbo Tang ◽  
Jian He ◽  
Tao Huang ◽  
Zhijie Bai ◽  
Chaojie Wang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mouse Model ◽  
Hematopoietic Stem Cells ◽  
Fetal Liver ◽  
Lineage Tracing ◽  
Genetic Lineage ◽  
Hematopoietic Stem ◽  
Genetic Lineage Tracing

In the aorta-gonad-mesonephros (AGM) region of mouse embryos, pre-hematopoietic stem cells (pre-HSCs) are generated from rare and specialized hemogenic endothelial cells (HECs) via endothelial-to-hematopoietic transition, followed by maturation into bona fide hematopoietic stem cells (HSCs). As HECs also generate a lot of hematopoietic progenitors not fated to HSCs, powerful tools that are pre-HSC/HSC-specific become urgently critical. Here, using the gene knockin strategy, we firstly developed an Hlf-tdTomato reporter mouse model and detected Hlf-tdTomato expression exclusively in the hematopoietic cells including part of the immunophenotypic CD45– and CD45+ pre-HSCs in the embryonic day (E) 10.5 AGM region. By in vitro co-culture together with long-term transplantation assay stringent for HSC precursor identification, we further revealed that unlike the CD45– counterpart in which both Hlf-tdTomato-positive and negative sub-populations harbored HSC competence, the CD45+ E10.5 pre-HSCs existed exclusively in Hlf-tdTomato-positive cells. The result indicates that the cells should gain the expression of Hlf prior to or together with CD45 to give rise to functional HSCs. Furthermore, we constructed a novel Hlf-CreER mouse model and performed time-restricted genetic lineage tracing by a single dose induction at E9.5. We observed the labeling in E11.5 AGM precursors and their contribution to the immunophenotypic HSCs in fetal liver (FL). Importantly, these Hlf-labeled early cells contributed to and retained the size of the HSC pool in the bone marrow (BM), which continuously differentiated to maintain a balanced and long-term multi-lineage hematopoiesis in the adult. Therefore, we provided another valuable mouse model to specifically trace the fate of emerging HSCs during development.

Evaluation of Methods To Assess the Biofilm-Forming Ability of Listeria monocytogenes

2012 ◽  
Vol 75 (8) ◽  
pp. 1411-1417 ◽  
Author(s):  
ANTÓNIO LOURENÇO ◽  
FRANCISCO REGO ◽  
LUISA BRITO ◽  
JOSEPH F. FRANK
Keyword(s):  
Stainless Steel ◽  
Listeria Monocytogenes ◽  
High Throughput ◽  
Biofilm Formation ◽  
High Throughput Screening ◽  
Screening Methods ◽  
Genetic Lineage ◽  
Production Lines ◽  
Genetic Characteristics

The contamination of ready-to-eat products with Listeria monocytogenes has been related to the presence of biofilms in production lines, as biofilms protect cells from chemical sanitizers. The ability of L. monocytogenes to produce biofilms is often evaluated using in vitro methodologies. This work aims to compare the most frequently used methodologies, including high-throughput screening methods based on microplates (crystal violet and the Calgary Biofilm Device) and methods based on CFU enumeration and microscopy after growth on stainless steel. Thirty isolates with diverse origins and genetic characteristics were evaluated. No (or low) correlations between methods were observed. The only significant correlation was found between the methods using stainless steel. No statistically significant correlation (P > 0.05) was detected among genetic lineage, serovar, and biofilm-forming ability. Because results indicate that biofilm formation is influenced by the surface material, the extrapolation of results from high-throughput methods using microplates to more industrially relevant surfaces should be undertaken with caution.

scholarly journals The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale

2018 ◽  
Vol 84 (11) ◽  
Author(s):  
B. Taboada ◽  
P. Isa ◽  
A. L. Gutiérrez-Escolano ◽  
R. M. del Ángel ◽  
J. E. Ludert ◽  
...  
Keyword(s):  
Fish Species ◽  
Phylogenetic Trees ◽  
Biological Diversity ◽  
Chihuahuan Desert ◽  
Geographic Scale ◽  
Geographic Structure ◽  
Virus Diversity ◽  
Intestinal Contents ◽  
Cuatro Ciénegas ◽  
Cuatro Ciénegas Basin

ABSTRACT The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare. IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its “lost world” status.

Research Tools and Methods for the Analysis of Microbiota in Dairy Products

2018 ◽  
pp. 23-53 ◽  
Author(s):  
Sylvia Klaubauf ◽  
Frank J. J. Segers
Keyword(s):  
Dna Sequencing ◽  
Production Process ◽  
Microbial Communities ◽  
Dairy Products ◽  
Starter Cultures ◽  
Direct Pcr ◽  
Culture Independent ◽  
Profiling Techniques ◽  
Tools And Methods ◽  
Culture Dependent

Microorganisms play important roles in dairy products. They can be a source of spoilage, or they promote health or cause diseases. In dairy fermentations, microorganisms are of great importance due to their function as starter cultures and during the production process of dairy products. In order to better understand and improve the process, it is essential to identify the species that are involved and to monitor the development of microbial communities. There are several different approaches for the detection and analysis of the microbiota. The methods can be culture dependent and, for example, make use of morphological and physiological characters or DNA sequencing. Culture-independent methods include direct PCR and qPCR, but also electrophoresis-based profiling techniques as well as metagenomics. Descriptions of relevant methods are provided and their applications are discussed in this chapter.

scholarly journals Diazotrophic Anaeromyxobacter Isolates from Soils

2020 ◽  
Vol 86 (16) ◽  
Author(s):  
Yoko Masuda ◽  
Haruka Yamanaka ◽  
Zhen-Xing Xu ◽  
Yutaka Shiratori ◽  
Toshihiro Aono ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Paddy Soils ◽  
Soil Environment ◽  
Soil Dna ◽  
Content Type ◽  
Environmental Function ◽  
Culture Independent ◽  
Nitrogenase Genes ◽  
Dependent Growth

ABSTRACT Biological nitrogen fixation is an essential reaction in a major pathway for supplying nitrogen to terrestrial environments. Previous culture-independent analyses based on soil DNA/RNA/protein sequencing could globally detect the nitrogenase genes/proteins of Anaeromyxobacter (in the class Deltaproteobacteria), commonly distributed in soil environments and predominant in paddy soils; this suggests the importance of Anaeromyxobacter in nitrogen fixation in soil environments. However, direct experimental evidence is lacking; there has been no research on the genetic background and ability of Anaeromyxobacter to fix nitrogen. Therefore, we verified the diazotrophy of Anaeromyxobacter based on both genomic and culture-dependent analyses using Anaeromyxobacter sp. strains PSR-1 and Red267 isolated from soils. Based on the comparison of nif gene clusters, strains PSR-1 and Red267 as well as strains Fw109-5, K, and diazotrophic Geobacter and Pelobacter in the class Deltaproteobacteria contain the minimum set of genes for nitrogenase (nifBHDKEN). These results imply that Anaeromyxobacter species have the ability to fix nitrogen. In fact, Anaeromyxobacter PSR-1 and Red267 exhibited N2-dependent growth and acetylene reduction activity (ARA) in vitro. Transcriptional activity of the nif gene was also detected when both strains were cultured with N2 gas as a sole nitrogen source, indicating that Anaeromyxobacter can fix and assimilate N2 gas by nitrogenase. In addition, PSR-1- or Red267-inoculated soil showed ARA activity and the growth of the inoculated strains on the basis of RNA-based analysis, demonstrating that Anaeromyxobacter can fix nitrogen in the paddy soil environment. Our study provides novel insights into the pivotal environmental function, i.e., nitrogen fixation, of Anaeromyxobacter, which is a common soil bacterium. IMPORTANCE Anaeromyxobacter is globally distributed in soil environments, especially predominant in paddy soils. Current studies based on environmental DNA/RNA analyses frequently detect gene fragments encoding nitrogenase of Anaeromyxobacter from various soil environments. Although the importance of Anaeromyxobacter as a diazotroph in nature has been suggested by culture-independent studies, there has been no solid evidence and validation from genomic and culture-based analyses that Anaeromyxobacter fixes nitrogen. This study demonstrates that Anaeromyxobacter harboring nitrogenase genes exhibits diazotrophic ability; moreover, N2-dependent growth was demonstrated in vitro and in the soil environment. Our findings indicate that nitrogen fixation is important for Anaeromyxobacter to survive under nitrogen-deficient environments and provide a novel insight into the environmental function of Anaeromyxobacter, which is a common bacterium in soils.

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