Advancements in assessing soil health through functional traits and energy flow analysis of soil

We examined the development of soil nematodes ecological indices from the perspective off unctionaltraits.We found that soil nematode energy flow analyses based on multiple functional traits quantify the dynamics of energy flow across multipletrophic levels to provide a more comprehensive perspective.We conducted comparative analyses of the sensitivities of NMF and energy flow to verify that the energy flow analyses are more sensitive and have greater potential to reveal soil health and ecosystem function.Future in-depth studies of functional traits and energy flow analysis can help us achieve informed soil management practices,sustainable agriculture,andhealthiersoilecosystems.nignerEauc Tess CT Nematode ecological index based on functional traits:MI El,S,BI,C1 NMF Bongen.1990 Ferrisetal,2001 Ferris,2010 energs low analysis of soil nematodes Compare thecological index(NMf)and Bacterivores(Ba)Functional traits Energy flux Fungihores(Fn)rahn Soilnematodes latitude Lindicator Plant-parasites(PP)PF Energflus Soilhealth Omnivores-predators(oP)latitude Energy flow analysis of soil nematodes:By quantifying energy fux among trophic groups Barbes et al.,2014,2018 This paper examines the development of ecological indices for soil nematodes from the perspective of functional traits.It emphasizes the increasing significance of integrating multiple functional traits to achieve a more accurate assessment of soil health.Ecological indices based on life history strategies,feeding habits,and body size provide useful tools for assessing soil health.However,these indices do not fully capture the dynamics ofenergyflow across multiple-trophic levels inthesoil foodweb,which is critical fora deeperunderstanding of the intrinsic properties of soil health.By combining functional traits such as functional group,body size,feeding preference and metabolic rate,nematode energy flow analyses provide a more comprehensive perspective.This approach establishes a direct correlation between changes in the morphology,physiology,and metabolism of soil organisms and alterations in their habitat environment.We conducted comparative analyses of the sensitivity of nematode metabolic footprints and energy flow to latitudinal variation using a nematode dataset from the northeastern black soil region in China.The findings suggest that energy flow analyses are more sensitive to latitude and have greater potential to reveal soil health and ecosystem function.Therefore,future research should prioritize the development of automated and efficient methods for analyzing nematode traits.This will enhance the application of energy flow analyses in nematode food webs and support the development of sustainable soil management and agriculturalpractices.

Phylogeny,ecology and taxonomy of systemic pathogens and their relatives in Ajellomycetaceae(Onygenales):Blastomyces,Emergomyces,Emmonsia,Emmonsiellopsis

The family Ajellomycetaceae(Onygenales)includes mammal-associated pathogens within the genera Blastomyces,Emmonsia,Histoplasma and Paracoccidioides,as well as the recently described genera,Emergomyces that causes disease in immunocompromised hosts,and Emmonsiellopsis,known only from soil.To further assess the phylogenetic relationships among and between members of these genera and several previously undescribed species,we sequenced and analyzed the DNA-directed RNA polymerase II(rPB2),translation elongation factor 3-a(TEF3),b-tubulin(TUB2),28S large subunit rDNA(LSU)and the internal transcribed spacer regions(ITS)in 68 strains,in addition to morphological and physiological investigations.To better understand the thermal dimorphism among these fungi,the dynamic process of transformation from mycelial to yeast-like or adiaspore-like forms was also assessed over a range of temperatures(6–42C).Molecular data resolved the relationships and recognized five major well-supported lineages that correspond largely to the genus level.Emmonsia,typified by Emmonsia parva,is a synonym of Blastomyces that also accommodates Blastomyces helicus(formerly Emmonsia helica).Emmonsia crescens is phylogenetically distinct,and found closely related to a single strain from soil without known etiology.Blastomyces silverae,Emergomyces canadensis,Emergomyces europaeus and Emmonsia sola are newly described.Almost all of the taxa are associated with human and animal disease.Emmonsia crescens,B.dermatitidis and B.parvus are prevalently associated with pulmonary disease in humans or animals.Blastomyces helicus,B.percursus,Emergomyces africanus,Es.canadensis,Es.europaeus,Es.orientalis and Es.pasteurianus(formerly Emmonsia pasteuriana)are predominantly found in human hosts with immune disorders;no animal hosts are known for these species except B.helicus.

The evolving species concepts used for yeasts:from phenotypes and genomes to speciation networks

Here we review how evolving species concepts have been applied to understand yeast diversity.Initially,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,and growth profiles.Later the biological species concept was added,which applied data from mating experiments.Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology,leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA.At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy,including yeasts,because various studies revealed a relatively good correlation between the biological species concept and sequence divergence.The application of genome information is becoming increasingly common,and we strongly recommend the use of complete,rather than draft genomes to improve our understanding of species and their genome and genetic dynamics.Complete genomes allow in-depth comparisons on the evolvability of genomes and,consequently,of the species to which they belong.Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts.Note that hybrids may greatly differ in their post-hybridization development.Future in-depth studies,initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes,such as hybridization.

Correction to:The evolving species concepts used for yeasts:from phenotypes and genomes to speciation networks

The name of the second author was incorrectly captured in the initial online publication,and due to an error at the proofs stage,several proof corrections had been left undone.The original online article has been corrected.

Delimiting species in Basidiomycota:a review

Species delimitation is one of the most fundamental processes in biology.Biodiversity undertakings,for instance,require explicit species concepts and criteria for species delimitation in order to be relevant and translatable.However,a perfect species concept does not exist for Fungi.Here,we review the species concepts commonly used in Basidiomycota,the second largest phylum of Fungi that contains some of the best known species of mushrooms,rusts,smuts,and jelly fungi.In general,best practice is to delimitate species,publish new taxa,and conduct taxonomic revisions based on as many independent lines of evidence as possible,that is,by applying a so-called unifying(or integrative)conceptual framework.However,the types of data used vary considerably from group to group.For this reason we discuss the different classes of Basidiomycota,and for each provide:(i)a general introduction with difficulties faced in species recognition,(ii)species concepts and methods for species delimitation,and(iii)community recommendations and conclusions.