scholarly journals Broad geographical and ecological diversity from similar genomic toolkits in the ascomycete genus Tetracladium

2020 ◽  
Author(s):  
Jennifer L. Anderson ◽  
Ludmila Marvanová
Keyword(s):  
Extreme Environments ◽  
Pectate Lyase ◽  
Aquatic Hyphomycetes ◽  
Genomic Diversity ◽  
Ecological Diversity ◽  
Carbohydrate Active Enzymes ◽  
Cold Adapted ◽  
The World ◽  
Genome Content ◽  
Stream Food Webs

ABSTRACTThe ascomycete genus Tetracladium is best known for containing aquatic hyphomycetes, which are important decomposers in stream food webs. However, some species of Tetracladium are thought to be multifunctional and are also endobionts in plants. Suprisingly, Tetracladium sequences are increasingly being reported from metagenomics and metabarcoding studies of both plants and soils world-wide. It is not clear how these sequences are related to the described species and little is known about the non-aquatic biology of these fungi. Here, the genomes of 24 Tetracladium strains, including all described species, were sequenced and used to resolve relationships among taxa and to improve our understanding of ecological and genomic diversity in this group. All genome-sequenced Tetracladium fungi form a monophyletic group. Conspecific strains of T. furcatum from both aquatic saprotrophic and endobiont lifestyles and a putative cold-adapted clade are identified. Analysis of ITS sequences from water, soil, and plants from around the world reveals that multifunctionality may be widespread through the genus. Further, frequent reports of these fungi from extreme environments suggest they may have important but unknown roles in those ecosystems. Patterns of predicted carbohydrate active enzymes (CAZyme) and secondary metabolites in the Tetracladium genomes are more similar to each other than to other ascomycetes, regardless of ecology, suggesting a strong role for phylogeny shaping genome content in the genus. Tetracladium genomes are enriched for pectate lyase domains (including PL3-2), GH71 α-1,3-glucanase domains and CBM24 α-1,3-glucan/mutan binding modules, and both GH32 and CBM38, inulinase and inulin binding modules. These results indicate that these fungi are well-suited to digesting pectate and pectin in leaves when living as aquatic hyphomycetes, and inulin when living as root endobionts. Enrichment for α-1,3-glucanase domains may be associated with interactions with biofilm forming microorganisms in root and submerged leaf environments.

scholarly journals Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dennie te Molder ◽  
Wasin Poncheewin ◽  
Peter J. Schaap ◽  
Jasper J. Koehorst
Keyword(s):  
Machine Learning ◽  
Plant Pathogens ◽  
De Novo ◽  
Classification Algorithms ◽  
Learning Approaches ◽  
Enabling Factors ◽  
Essential Step ◽  
The World ◽  
Genome Content

Abstract Background The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype. Until now such approaches to the pathogenomics of Xanthomonas strains have been hampered by the fragmentation of information regarding pathogenicity of individual strains over many studies. Unification of this information into a single resource was therefore considered to be an essential step. Results Mining of 39 papers considering both plant-associated phenotypes, allowed for a phenotypic classification of 578 Xanthomonas strains. For 65 plant-pathogenic and 53 non-pathogenic strains the corresponding genomes were available and de novo annotated for the presence of Pfam protein domains used as features to train and compare three ML classification algorithms; CART, Lasso and Random Forest. Conclusion The literature resource in combination with recursive feature extraction used in the ML classification algorithms provided further insights into the virulence enabling factors, but also highlighted domains linked to traits not present in pathogenic strains.

scholarly journals Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature

2020 ◽  
Vol 8 (6) ◽  
pp. 906 ◽  
Author(s):  
Francisco L. Massello ◽  
Chia Sing Chan ◽  
Kok-Gan Chan ◽  
Kian Mau Goh ◽  
Edgardo Donati ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Metabolic Profile ◽  
Hot Springs ◽  
Meta Analysis ◽  
Extreme Environments ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Phylogenetic Distance ◽  
Microbial Profile ◽  
The World

The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities’ profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed.

scholarly journals Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments

FEBS Journal ◽  
2019 ◽  
Vol 287 (6) ◽  
pp. 1116-1137 ◽  
Author(s):  
Andrea Strazzulli ◽  
Beatrice Cobucci‐Ponzano ◽  
Roberta Iacono ◽  
Rosa Giglio ◽  
Luisa Maurelli ◽  
...  
Keyword(s):  
Extreme Environments ◽  
Carbohydrate Active Enzymes

scholarly journals Forecasting range shifts of a cold-adapted species under climate change: are genomic and ecological diversity within species crucial for future resilience?

Ecography ◽  
2018 ◽  
Vol 41 (8) ◽  
pp. 1357-1369 ◽  
Author(s):  
Spyros Theodoridis ◽  
Theofania S. Patsiou ◽  
Christophe Randin ◽  
Elena Conti
Keyword(s):  
Climate Change ◽  
Range Shifts ◽  
Ecological Diversity ◽  
Cold Adapted

scholarly journals Genomic Diversity ofLactobacillus salivarius

2010 ◽  
Vol 77 (3) ◽  
pp. 954-965 ◽  
Author(s):  
Emma J. Raftis ◽  
Elisa Salvetti ◽  
Sandra Torriani ◽  
Giovanna E. Felis ◽  
Paul W. O'Toole
Keyword(s):  
Hot Spots ◽  
Gene Clusters ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Phenotypic Traits ◽  
Lactobacillus Salivarius ◽  
Genome Content ◽  
High Level ◽  
Selection Of

ABSTRACTStrains ofLactobacillus salivariusare increasingly employed as probiotic agents for humans or animals. Despite the diversity of environmental sources from which they have been isolated, the genomic diversity ofL. salivariushas been poorly characterized, and the implications of this diversity for strain selection have not been examined. To tackle this, we applied comparative genomic hybridization (CGH) and multilocus sequence typing (MLST) to 33 strains derived from humans, animals, or food. The CGH, based on total genome content, including small plasmids, identified 18 major regions of genomic variation, or hot spots for variation. Three major divisions were thus identified, with only a subset of the human isolates constituting an ecologically discernible group. Omission of the small plasmids from the CGH or analysis by MLST provided broadly concordant fine divisions and separated human-derived and animal-derived strains more clearly. The two gene clusters for exopolysaccharide (EPS) biosynthesis corresponded to regions of significant genomic diversity. The CGH-based groupings of these regions did not correlate with levels of production of bound or released EPS. Furthermore, EPS production was significantly modulated by available carbohydrate. In addition to proving difficult to predict from the gene content, EPS production levels correlated inversely with production of biofilms, a trait considered desirable in probiotic commensals.L. salivariusdisplays a high level of genomic diversity, and while selection ofL. salivariusstrains for probiotic use can be informed by CGH or MLST, it also requires pragmatic experimental validation of desired phenotypic traits.

Living Waters

2013 ◽  
Author(s):  
Nick Romanowski
Keyword(s):  
Natural History ◽  
Extreme Environments ◽  
Inland Waters ◽  
Ecological Change ◽  
The World ◽  
The Many ◽  
The Tropics

Wetlands are often seen as the ultimate symbol of beauty and tranquillity, their clear waters sheltering mysterious animals in a world where change is gentle and slow, from dragonflies skimming above their own reflections to the fishes glimpsed briefly below. Yet Australian wetlands are among the most varied and changeable habitats found anywhere, and the many creatures that live out their lives in and around water are superbly adapted to some of the most unpredictable ecosystems in the world. This book follows the diverse common themes and patterns that link inland waters from Tasmania to the tropics. It shows how cycles of change, the ways that different wetland animals travel through and between wetlands, and the interactions of the animals themselves create an ever-changing ecological kaleidoscope. Drawing on what is known of the biology, ecology and even the genetics of many of the most abundant, widespread and successful groups of animals, the author shows similarities to wetlands in other parts of the world, as well as some of the more extreme environments and specialised animals that are unique to this continent. Far more than a natural history, Living Waters explains the underlying forces that drive ecological change and movement in Australian wetlands, from the particular needs and habits of some specialised waterbirds to swarms of dragonflies and damselflies that may flourish for a few months before disappearing for years, and fishes found gasping in drying pools far from the nearest permanent water just hours after a desert deluge. 2014 Whitley Award Commendation for Aquatic Biology.

Effects on Fertility and Reproductive Behavior From Environmental Contaminants in Extreme Environments

2021 ◽  
pp. 206-225
Author(s):  
Irfan Ashraf Badroo ◽  
Ashiq Hussain Khanday ◽  
Suriya Ashraf Badroo ◽  
Saba Khursheed Khan ◽  
Irshad Aziz Malik ◽  
...  
Keyword(s):  
Literature Review ◽  
Reproductive Behavior ◽  
Environmental Contaminants ◽  
Extreme Environments ◽  
Female Partner ◽  
Nano Materials ◽  
Industrial Chemicals ◽  
Reproductive Disorders ◽  
Huge Number ◽  
The World

Human infertility is increasing at an alarming rate and has affected nearly 12% of reproductive aged couples worldwide. Various reasons have been linked to its cause, besides the age of female partner, a huge number of environmental contaminants produced and used by humans throughout the world are one of the reasons for growing the infertility rate. Their exposure is virtually unavoidable. The literature review provides an overview regarding the effect of chemical agents on fertility. The environmental contaminants included in this review are plastics, pesticides, phthalates, metals, industrial chemicals, endocrine disrupters, and nano materials. The goal is to discuss the association between environmental contaminants and reproductive disorders with particular emphasis on infertility.

Industrial Applications of Enzymes From Extremophiles

2022 ◽  
pp. 207-232
Author(s):  
Prashant Satishbhai Arya ◽  
Shivani Maheshkumar Yagnik ◽  
Rakeshkumar Ramanlal Panchal ◽  
Kiransinh Narendrasinh Rajput ◽  
Vikram Hiren Raval
Keyword(s):  
Asymmetric Catalysis ◽  
Organic Solvents ◽  
Environmental Remediation ◽  
Extreme Environments ◽  
Industrial Applications ◽  
Hazardous Substance ◽  
Cold Adapted ◽  
Food Industries ◽  
Extremophilic Microorganisms ◽  
Area Of Application

Extremophilic microorganisms have developed a variety of molecular tactics to exist in extreme environments. Researchers are fascinated by extremophiles and unearth various enzymes from these fascinating microbes. Extremozymes are astonishing biocatalysts with distinctive properties of catalysis and stability under a multitude of daunting conditions of salt, pH, organic solvents, and temperature, which open up new possibilities for biocatalysis and biotransformation and outcompetes mesophilic counterparts. Biotechnological implications include simple, immobilized, as well as whole-cell applications. Stability in organic solvents adds to the asymmetric catalysis and thereby exemplifies the applicability of extremozymes and in fostering biobased economies. Marine, cold-adapted enzymes, and those that help in the removal of a toxic hazardous substance from the environment are obvious choices for food industries and bioremediation. The major area of application and research emphasis includes textile, detergents, food, dairy, agriculture, and environmental remediation.

scholarly journals Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum

2019 ◽  
Vol 7 (11) ◽  
pp. 527 ◽  
Author(s):  
Konstantin V. Moiseenko ◽  
Olga A. Glazunova ◽  
Natalia V. Shakhova ◽  
Olga S. Savinova ◽  
Daria V. Vasina ◽  
...  
Keyword(s):  
De Novo ◽  
White Rot ◽  
Wood Decomposition ◽  
Carbohydrate Active Enzymes ◽  
Climatic Zones ◽  
Substrate Preferences ◽  
The World ◽  
Advanced Stages ◽  
Fungal Adaptation ◽  
Enzymatic Mechanisms

Steccherinum ochraceum is a white rot basidiomycete with wide ecological amplitude. It occurs in different regions of Russia and throughout the world, occupying different climatic zones. S. ochraceum colonizes stumps, trunks, and branches of various deciduous (seldom coniferous) trees. As a secondary colonizing fungus, S. ochraceum is mainly observed at the late decay stages. Here, we present the de novo assembly and annotation of the genome of S. ochraceum, LE-BIN 3174. This is the 8th published genome of fungus from the residual polyporoid clade and the first from the Steccherinaceae family. The obtained genome provides a first glimpse into the genetic and enzymatic mechanisms governing adaptation of S. ochraceum to an ecological niche of pre-degraded wood. It is proposed that increased number of carbohydrate-active enzymes (CAZymes) belonging to the AA superfamily and decreased number of CAZymes belonging to the GH superfamily reflects substrate preferences of S. ochraceum. This proposition is further substantiated by the results of the biochemical plate tests and exoproteomic study, which demonstrates that S. ochraceum assumes the intermediate position between typical primary colonizing fungi and litter decomposers or humus saprotrophs. Phylogenetic analysis of S. ochraceum laccase and class II peroxidase genes revealed the distinct evolutional origin of these genes in the Steccherinaceae family.

scholarly journals Plant growth promoting traits of psychrotolerant bacteria: A boon for agriculture in hilly terrains

2018 ◽  
Vol 5 (1) ◽  
pp. 24-28 ◽  
Author(s):  
B Patni ◽  
A S Panwar ◽  
P Negi ◽  
Gopal Krishna Joshi
Keyword(s):  
Low Temperature ◽  
Plant Growth ◽  
Extreme Environments ◽  
Agricultural Practices ◽  
Plant Growth Promoting Bacteria ◽  
Psychrotolerant Bacteria ◽  
The World ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Plant Growth Promoting Traits

Plant growth promoting bacteria (PGPB) are well known to promote plant growth in a number of ways. It is important to study plant growth promoting potential of bacteria capable of growing in extreme environments to establish their role in promoting agricultural yield under harsh conditions. Psychrophilic or psychrotolerant bacteria with plant growth promoting traits may improve the quality of agricultural practices in hilly terrain. The agricultural importance of such microbes stems from the fact that the world over temperate agro-ecosystems are characterized by low temperatures and short growing seasons that subject both plant and microbial life to cold temperature induced stress. Hence, there is a need to identify potential microbes that retain their functional traits under low temperature conditions. Such microbes can be used to enhance the agricultural yields in low temperature areas of the world. This review describes plant growth promoting activities identified in cold adapted bacteria.

Sign in / Sign up

Export Citation Format

Share Document