scholarly journals Remarkably coherent population structure for a dominant Antarctic Chlorobium species

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Pratibha Panwar ◽  
Michelle A. Allen ◽  
Timothy J. Williams ◽  
Sabrina Haque ◽  
Sarah Brazendale ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Species ◽  
Genomic Variation ◽  
Seasonal Abundance ◽  
Energetic Cost ◽  
Broad Host Range ◽  
Sulphur Bacteria ◽  
Green Sulphur ◽  
Vestfold Hills ◽  
Marine Basins

Abstract Background In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby “feeding” ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. Results A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108 cells ml−1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. Conclusion The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species.

scholarly journals Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoting Xia ◽  
Shunjin Zhang ◽  
Huaju Zhang ◽  
Zijing Zhang ◽  
Ningbo Chen ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
System Response ◽  
Whole Genome ◽  
Population Structure Analysis ◽  
Native Cattle ◽  
Genomic Regions

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

Reply to the comment by Morales et al. on “Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species”

2021 ◽  
pp. 423-432
Author(s):  
C.L. Lausen ◽  
Michael F. Proctor ◽  
David Paetkau ◽  
David W. Nagorsen ◽  
Purnima Govindarajulu ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Single Species ◽  
Distinct Species ◽  
Background Information ◽  
Distribution Data ◽  
Supporting Evidence ◽  
Post Mortem ◽  
The Impact ◽  
New Evidence

A.E. Morales et al. (2021. Can. J. Zool. 99(5): 415–422) provided no new evidence to alter the conclusions of C.L. Lausen et al. (2019. Can. J. Zool. 97(3): 267–279). We present background information, relevant comparisons, and clarification of analyses to further strengthen our conclusions. The genesis of the original “evotis–keenii” study in British Columbia (Canada) was to differentiate Myotis keenii (Merriam, 1895) (Keen’s myotis), with one of the smallest North American bat distributions, from sympatric Myotis evotis (H. Allen, 1864) (long-eared myotis), using something other than the suggested post-mortem skull size comparison, but no differentiating trait could be found, leading to the molecular genetics examination of C.L. Lausen et al. (2019). We present cumulative data that rejects the 1979 hypothesis of M. keenii as a distinct species. A.E. Morales et al. (2021) inaccurately portray C.L. Lausen et al.’s (2019) question and results; present inaccurate morphological and outdated distribution data; overstate the impact of homoplasy without supporting evidence; and misinterpret evidence of population structure.

scholarly journals Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Pratibha Panwar ◽  
Michelle A. Allen ◽  
Timothy J. Williams ◽  
Alyce M. Hancock ◽  
Sarah Brazendale ◽  
...  
Keyword(s):  
Microbial Community ◽  
Carbon Fixation ◽  
Negative Impact ◽  
Green Sulfur Bacteria ◽  
Seasonal Abundance ◽  
Light Cycle ◽  
Video Footage ◽  
Cold Environments ◽  
Vestfold Hills ◽  
Global Biogeochemical Cycles

Abstract Background Cold environments dominate the Earth’s biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000–7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles. Results The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts. Conclusion Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems.

Wastewater treatment mechanisms in anoxic stabilization ponds

1996 ◽  
Vol 33 (7) ◽  
pp. 125-132 ◽  
Author(s):  
A. Almasi ◽  
M. B. Pescod
Keyword(s):  
Wastewater Treatment ◽  
Hydrogen Sulphide ◽  
Biological Activities ◽  
Euphotic Zone ◽  
Methanogenic Bacteria ◽  
Stabilization Ponds ◽  
Physico Chemical ◽  
Sulphur Bacteria ◽  
Green Sulphur ◽  
Treatment Mechanisms

Studies on the performance of wastewater stabilization ponds operating in the “grey” area of organic loading between fully anaerobic and facultative conditions show that organic matter removal is still satisfactory. The results obtained revealed that wastewater treatment mechanisms are mainly based on biochemical reactions in the anoxic system. Although physico-chemical mechanisms were not negligible, algal activities in the presence of light proved to be important in the surface layer of the pond and facultative bacteria were working mutually with the algae. Motile flagellate algae (Euglena and Chlamydomonas) were the only species found to exist under anoxic conditions. It was also determined that sulphate-reducing bacteria predominated in the lower volume of the anoxic ponds, rather than acidogenic bacteria, and this caused sulphide and hydrogen sulphide build-up in the pond's contents. The bottom volume of the ponds and the benthic sludge in laboratory-scale anoxic ponds contained acid producers and methanogenic bacteria causing the release of biogas. It is hypothesized that phototrophic bacteria (purple sulphur-, green sulphur- and purple non-sulphur bacteria) act as a biological filter to oxidize sulphide and hydrogen sulphide in the euphotic zone of the anoxic ponds. As a consequence of the latter biological activities, anoxic ponds are likely to prove viable alternatives to anaerobic and facultative ponds, where odour nuisance and high land requirements, respectively, are to be avoided.

scholarly journals Variation Profile of the Orthotospovirus Genome

Pathogens ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 521 ◽  
Author(s):  
Deepti Nigam ◽  
Hernan Garcia-Ruiz
Keyword(s):  
Intergenic Region ◽  
Dynamic Structure ◽  
Genomic Variation ◽  
Broad Host Range ◽  
Arms Races ◽  
Viral Genomes ◽  
Genetic Components ◽  
The Family ◽  
Rapid Changes ◽  
Hairpin Secondary Structure

Orthotospoviruses are plant-infecting members of the family Tospoviridae (order Bunyavirales), have a broad host range and are vectored by polyphagous thrips in a circulative-propagative manner. Because diverse hosts and vectors impose heterogeneous selection constraints on viral genomes, the evolutionary arms races between hosts and their pathogens might be manifested as selection for rapid changes in key genes. These observations suggest that orthotospoviruses contain key genetic components that rapidly mutate to mediate host adaptation and vector transmission. Using complete genome sequences, we profiled genomic variation in orthotospoviruses. Results show that the three genomic segments contain hypervariable areas at homologous locations across species. Remarkably, the highest nucleotide variation mapped to the intergenic region of RNA segments S and M, which fold into a hairpin. Secondary structure analyses showed that the hairpin is a dynamic structure with multiple functional shapes formed by stems and loops, contains sites under positive selection and covariable sites. Accumulation and tolerance of mutations in the intergenic region is a general feature of orthotospoviruses and might mediate adaptation to host plants and insect vectors.

scholarly journals Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal Genus Botrytis

2020 ◽  
Vol 12 (12) ◽  
pp. 2491-2507
Author(s):  
Claudio A Valero-Jiménez ◽  
Maikel B F Steentjes ◽  
Jason C Slot ◽  
Xiaoqian Shi-Kunne ◽  
Olga E Scholten ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Gene Clusters ◽  
Single Species ◽  
White Rot ◽  
White Rot Fungus ◽  
Broad Host Range ◽  
Allium Species ◽  
Sclerotium Cepivorum ◽  
Single Host ◽  
Long Read

Abstract Fungi of the genus Botrytis infect >1,400 plant species and cause losses in many crops. Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a single host. Long-read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained <100 contigs, with the Botrytis aclada genome assembled in 16 gapless chromosomes. The core genome and pan-genome of 16 Botrytis species were defined and the secretome, effector, and secondary metabolite repertoires analyzed. Among those genes, none is shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8–39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with ten other Botrytis species (nonpathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and Botrytis sinoallii were acquired by horizontal transfer from taxa within the same genus.

The meromictic lakes and stratified marine basins of the Vestfold Hills, East Antarctica

1999 ◽  
Vol 11 (2) ◽  
pp. 175-192 ◽  
Author(s):  
John A.E. Gibson
Keyword(s):  
Ice Formation ◽  
Convection Cell ◽  
Meromictic Lakes ◽  
Surface Level ◽  
Thermohaline Convection ◽  
Vestfold Hills ◽  
Lower Water Level ◽  
The Stability ◽  
Wind Mixing ◽  
Marine Basins

Thirty-four permanently stratified water bodies were identified in a survey of the Vestfold Hills. Of these, 21 were lakes, six were seasonally isolated marine basins (SIMBs), and seven were marine basins with year round connection to the open ocean. The basins varied markedly in salinity (4 g l−1 to 235 g l−1), temperature (−14°C to 24°C), depth (5 m to 110 m), area (3.6 ha to 146 ha) and surface level (−30 m to 29 m above sea level). The stratification in all the basins was maintained by increases in salinity. During winter, a thermohaline convection cell was present in all lakes and SIMBs directly beneath the ice cover. These cells were the result of brine exclusion from the forming ice, and increased in density throughout winter, penetrating progressively deeper into the lake. Minimum stability, and therefore the maximum likelihood of turnover, occurred at the time of maximum ice formation in spring. At the end of the period of ice formation, the convection cell broke down, and stratification of the surface water occurred. When the ice melted completely, lenses of relatively fresh water capped the lakes, which reduced the effect of wind mixing. Net meltwater input increased the stability of the meromictic basins, while periods of lower water level resulted in deeper penetration of the thermohaline convection cell, increasing the possibility of turnover and destratification.

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