The ribosomal RNA (rrn) operon is a key suite of genes related to the production of protein synthesis machinery and thus to bacterial growth physiology. Experimental evidence has suggested an intrinsic relationship between the number of copies of this operon and environmental resource availability, especially the availability of phosphorus (P), because bacteria that live in oligotrophic ecosystems usually have few rrn operons and a slow growth rate. The Cuatro Ciénegas Basin (CCB) is a complex aquatic ecosystem that contains an unusually high microbial diversity that is able to persist under highly oligotrophic conditions. These environmental conditions impose a variety of strong selective pressures that shape the genome dynamics of their inhabitants. The genus Bacillus is one of the most abundant cultivable bacterial groups in the CCB and usually possesses a relatively large number of rrn operon copies (6–15 copies). The main goal of this study was to analyze the variation in the number of rrn operon copies of Bacillus in the CCB and to assess their growth-related properties as well as their stoichiometric balance (N and P content). We defined 18 phylogenetic groups within the Bacilli clade and documented a range of from six to 14 copies of the rrn operon. The growth dynamic of these Bacilli was heterogeneous and did not show a direct relation to the number of operon copies. Physiologically, our results were not consistent with the Growth Rate Hypothesis, since the copies of the rrn operon were decoupled from growth rate. However, we speculate that the diversity of the growth properties of these Bacilli as well as the low P content of their cells in an ample range of rrn copy number is an adaptive response to oligotrophy of the CCB and could represent an ecological mechanism that allows these taxa to coexist. These findings increase the knowledge of the variability in the number of copies of the rrn operon in the genus Bacillus and give insights about the physiology of this bacterial group under extreme oligotrophic conditions.
We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.
Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant marginalized environments. These structures are considered highly stable ecosystems. In this study, we evaluate the ecological stability of dome-forming microbial mats in a modern, water-level fluctuating, hypersaline pond located in the Cuatro Ciénegas Basin, Mexico. We conducted metagenomic sampling of the site from 2016 to 2019 and detected 2250 genera of Bacteria and Archaea, with only <20 belonging to the abundant taxa (>1%). The microbial community was dominated by Proteobacteria, Euryarchaeota, Bacteroidetes, Firmicutes, and Cyanobacteria, and was compositionally sensitive to disturbances, leading to high taxonomic replacement even at the phylum level, with a significant increase in Archaea from $$\sim $$ ∼ 1-4% to $$\sim $$ ∼ 33% throughout the 2016-2019 study period. Although a core community represented most of the microbial community (>75%), relative abundances shifted significantly between samples, as demonstrated by changes in the abundance of Coleofasciculus from 10.2% in 2017 to 0.05% in 2019. Although functional differences between seasons were subtle, co-occurrence networks suggest differential ecological interactions between the seasons, with the addition of a new module during the rainy season and the potential shift in hub taxa. Functional composition was slightly more similar between samples, but basic processes such as carbohydrate, amino acid, and nucleic acid metabolisms were widely distributed among samples. Major carbon fixation processes included sulfur oxidation, nitrogen fixation, and photosynthesis (both oxygenic and anoxygenic), as well as the Wood-Ljundgahl and Calvin cycles.
We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three megaplasmids. The genome analysis suggests the presence of enzymes that confer E. pavilionensis str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals and high ultraviolet B radiation. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina . We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated 29 from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three 30 megaplasmids. The genome analysis suggests the presence of enzymes that confer E.31 pavilionensis str. N139 the ability to grow under multiple environmental extreme conditions, 32 including high concentrations of different metals and high ultraviolet B radiation. Moreover, the 33 regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, 34 and that these pathways might be fundamental in the amino acid metabolism of the microbial 35 community from Laguna Negra, Argentina. The high altitude Andean Lakes (HAALs) from Puna, Argentina, are a group of lakes 53 located at 3000-6000 meters above sea level which are characterized by high ultraviolet (UV) 54 radiation and salinity, broad temperature variations, low nutrient concentrations and high 55 contents of metals and metalloids, mainly arsenic (Fernández-Zenoff et al., 2006; Fernández-56 Zenoff, Siñeriz & Farías, 2006;Dib et al., 2008;Ordoñez et al., 2009; 57 Albarracín et al., 2011; Belfiore, Ordoñez & Farías, 2013). These environmental conditions are 58 considered to be extreme and might resemble those of the Earth's early atmosphere, as has been 59 stated by NASA (Cabrol et al., 2007;Farías et al., 2009). Hence, these geographical areas have 60 been proposed for studies on astrobiology . Despite being oligotrophic and 61 hostile, a great microbial diversity has been found in the HAALs, where bacteria from the genus 62 Exiguobacterium are one of the dominant taxa (Ordoñez et al., 2009(Ordoñez et al., , 2013Sacheti et al., 2013). 63The Exiguobacterium genus, a sister clade to the Bacillus genus, is currently 64 underexplored, and molecular studies of this genus from different sources are limited 65 (Vishnivetskaya, Kathariou & Tiedje, 2009 Figure 1A shows the phylogenetic reconstruction of 147 all Exiguobacterium species from both clades. These analyses placed the strain N139 as most 148 similar to E. pavilionensis str. RW-2 (White III, Grassa & Suttle, 2013), which is coherent with 149 the average nucleotide identity (ANI) analyses (see below). ANI calculations were done for 150 N139 versus all other complete genomic sequences of Exiguobacterium, and these two strains, 151 along...
Background. Plants are commonly colonized by a wide diversity of microbial species and the relationships created can range from mutualistic through to parasitic. Microorganisms that typically form symptomless associations with internal plant tissues are termed endophytes. Endophytes associate with most plant species found in natural and managed ecosystems. They are extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Plant domestication has reduced endophyte diversity and therefore the wild relatives of many crop species remain untapped reservoirs of beneficial microbes. Brassica species display immense diversity and consequently provide the greatest assortment of products used by humans from a single plant genus important for agriculture, horticulture, bioremediation, medicine, soil conditioners, composting crops, and in the production of edible and industrial oils. Many endophytes are horizontally transmitted, but some can colonize the plant's reproductive tissues, and this gives these symbionts an efficient mechanism of propagation via plant seed (termed vertical transmission). Methods. This study surveyed 83 wild and landrace Brassica accessions composed of 14 different species with a worldwide distribution for seed-originating bacterial endophytes. Seed was stringently disinfected, sown within sterile tissue culture pots within a sterile environment and incubated. After approximately one-month, direct isolation techniques were used to recover bacterial endophytes from roots and shoots of symptomless plants. Bacteria were identified based on the PCR amplification of partial 16S rDNA gene sequences and annotated using the BLASTn program against the NCBI rRNA database. A diversity index was used as a quantitative measure to reflect how many different bacterial species there were in the seed-originating microbial community of the Brassica accessions sampled. Results. Bacterial endophytes were recovered from the majority of the Brassica accessions screened. 16S rDNA gene sequencing identified 19 different bacterial species belonging to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria with the most frequently isolated species being Methylobacterium fujisawaense, Stenotrophomonas rhizophila and Pseudomonas lactis. Methylobacterium was the dominant genus composing 56% of the culturable isolated bacterial community and was common in 77% of accessions possessing culturable bacterial endophytes. Two selected isolates of Methylobacterium significantly promoted plant growth when inoculated into a cultivar of oilseed rape and inhibited the growth of the pathogen Leptosphaeria maculans in dual culture. This is the first report that investigates the seed-originating endophytic microorganisms of wild Brassica species and highlights the Brassica microbiome as a resource for plant growth promoting bacteria and biological control agents.
Merino E, Farías ME, Latorre A, Souza V. (2017)
The simplest form of heterotrophy in the carbon cycle is to metabolize C1 compounds, this is a widely spread strategy that includes genus in different phyla inhabiting diverse environments that seem to have acquired the methanol dehydrogenase by horizontal gene transfer (HGT). The objective of this study was to isolate and explore the diversity of the ecological guild of methylotrophs in the water and riparian vegetation of the Churince system in the Cuatro Cienegas Basin (CCB), Coahuila, Mexico. Methylotrophy was verified by polymerase chain reaction (PCR) amplification of the mxaF gene that encodes the α-subunit of the enzyme methanol dehydrogenase (MDH), while phylogenetic affiliations were assigned following 16S rRNA phylogenetic analyses. Among the isolated strains we observed a phylogenetic association with a common species of Methylobacterium (M. radiotolerans). In addition, other methylotrophs were isolated, like Methylorubrum aminovorans, Methylorubrum extorquems and Methylophilus methylotrophus. Interestingly, we also isolated other strains able to grow in methanol and mxaF+, their 16S rRNA identified them as Jiella, Pseudomonas, Rhizobium, Serratia and Stenotrophomonas. This study addresses, for the first time, the diversity of cultivated methylotrophic bacteria within CCB and inserts this knowledge in the context of a total inventory of the microbiota in the site.
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