Substituting nitrogen and phosphorus fertilizer with optimal amount of crop straw improves rice grain yield,nutrient use efficiency and soil carbon sequestration

Crop straw return after harvest is considered an important way to achieve both agronomic and environmental benefits.However,the appropriate amount of straw to substitute for fertilizer remains unclear.A field experiment was performed from 2016 to 2018 to explore the effect of different amounts of straw to substitute for fertilizer on soil properties,soil organic carbon(SOC)storage,grain yield,yield components,nitrogen(N)use efficiency,phosphorus(P)use efficiency,N surplus,and P surplus after rice harvesting.Relative to mineral fertilization alone,straw substitution at 5 t ha^(-1)improved the number of spikelets per panicle,effective panicle,seed setting rate,1000-grain weight,and grain yield,and also increased the aboveground N and P uptake in rice.Straw substitution exceeding 2.5 t ha^(-1)increased the soil available N,P,and K concentrations as compared with mineral fertilization,and different amounts of straw substitution improved SOC storage compared with mineral fertilization.Furthermore,straw substitution at 5 t ha^(-1)decreased the N surplus and P surplus by up to 68.3 and 28.9%,respectively,compared to mineral fertilization.Rice aboveground N and P uptake and soil properties together contributed 19.3%to the variation in rice grain yield and yield components.Straw substitution at 5 t ha^(-1),an optimal fertilization regime,improved soil properties,SOC storage,grain yield,yield components,N use efficiency(NUE),and P use efficiency(PUE)while simultaneously decreasing the risk of environmental contamination.

National Forest Inventories capture the multifunctionality of managed forests in Germany

Background:Forests perform various important ecosystem functions that contribute to ecosystem services.In many parts of the world,forest management has shifted from a focus on timber production to multi-purpose forestry,combining timber production with the supply of other forest ecosystem services.However,it is unclear which forest types provide which ecosystem services and to what extent forests primarily managed for timber already supply multiple ecosystem services.Based on a comprehensive dataset collected across 150 forest plots in three regions differing in management intensity and species composition,we develop models to predict the potential supply of 13 ecosystem services.We use those models to assess the level of multifunctionality of managed forests at the national level using national forest inventory data.Results:Looking at the potential supply of ecosystem services,we found trade-offs(e.g.between both bark beetle control or dung decomposition and both productivity or soil carbon stocks)as well as synergies(e.g.for temperature regulation,carbon storage and culturally interesting plants)across the 53 most dominant forest types in Germany.No single forest type provided all ecosystem services equally.Some ecosystem services showed comparable levels across forest types(e.g.decomposition or richness of saprotrophs),while others varied strongly,depending on forest structural attributes(e.g.phosphorous availability or cover of edible plants)or tree species composition(e.g.potential nitrification activity).Variability in potential supply of ecosystem services was only to a lesser extent driven by environmental conditions.However,the geographic variation in ecosystem function supply across Germany was closely linked with the distribution of main tree species.Conclusions:Our results show that forest multifunctionality is limited to subsets of ecosystem services.The importance of tree species composition highlights that a lack of multifunctionality at the stand level can be compensated by managing forests at the landscape level,when stands of complementary forest types are combined.These results imply that multi-purpose forestry should be based on a variety of forest types requiring coordinated planning across larger spatial scales.

黄土区几种土壤培养过程中可溶性有机碳、氮含量及特性的变化

对不同地域农田和林地土壤进行35 d好气培养研究,结果表明:不同土壤培养过程中可溶性有机碳(SOC)含量呈明显下降,而可溶性有机氮(SON)含量却呈明显增加趋势。不同农田土壤相比,在培养起始时和培养过程中红油土SOC和SON的平均含量均高于黑垆土和淋溶褐土;同为黑垆土,林地土壤SOC和SON含量均明显高于相应农田土壤。与起始值相比,土壤培养后提取的可溶性有机物的UV280和HIXem(Hu-mification index)值均明显增加,其中HIXem值在培养的第8天和第35天时呈显著增加趋势。随着培养过程的持续,SOC/SON比值逐渐下降。相关分析发现,培养第35天时SOC的减少幅度与UV 280增加比例呈显著正相关;培养第8天时SOC的减少比例与起始HIXem值呈显著负相关。说明UV280和HIXem值可以在一定程度上反映可溶性有机物种类和结构特性的变化。

Preservation of nucleic acids by freeze-drying for next generation sequencing analyses of soil microbial communities

Aims Soil sample preservation is a challenging aspect in molecular studies on soil microbial communities.The demands for specialized sample storage equipment,chemicals and standardized protocols for nucleic acid extraction often require sample processing in a home laboratory that can be continents apart from sampling sites.Standard sampling procedures,especially when dealing with RNA,comprise immediate snap freezing of soils in liquid nitrogen and storage at−80℃until further processing.For these instances,organizing a reliable cooling chain to transport hundreds of soil samples between continents is very costly,if possible at all.In this study we tested the effect of soil sample preservation by freeze-drying with subsequent short-term storage at 4℃or ambient temperatures compared to−80℃freezing by comparative barcoding analyses of soil microbial communities.Methods Two grassland soil samples were collected in Central Germany in the Biodiversity Exploratory Hainich-Dün.Samples were freeze-dried or stored at−80℃as controls.Freeze-dried samples were stored at 4℃or ambient temperature.Investigated storage times for both storage temperatures were 1 and 7 days.Total DNA and RNA were extracted and bacterial and arbuscular mycorrhizal(AM)fungal communities were analyzed by amplicon 454 pyrosequencing of the 16S(V4-V5 variable region)and 18S(NS31-AM1 fragment)of ribosomal RNA(rRNA)marker genes,respectively.Important Findings Bacterial communities were sufficiently well preserved at the rDNA and rRNA level although storage effects showed as slightly decreased alpha diversity indices for the prolonged storage of freeze-dried samples for 7 days.AM fungal communities could be studied without significant changes at the rDNA and rRNA level.Our results suggest that proper sampling design followed by immediate freeze-drying of soil samples enables short-term transportation of soil samples across continents.

Direct comparison of culture-dependent and culture-independent molecular approaches reveal the diversity of fungal endophytic communities in stems of grapevine(Vitis vinifera)

Grapevines(Vitis vinifera)are colonized by ubiquitous microorganisms known as endophytes,which may have advantageous or neutral effects without causing disease symptoms.Certain endophytes are uncultivable,so culture-independent approaches such as next generation sequencing(NGS)can help for a better understanding of their ecology and distribution.To date,there are no studies which directly link NGS results with taxa derived from a culturing approach,integrating morphological and multi-gene phylogenetic analysis of endophytes.In this study,a culture-dependent and high-resolution culture-independent approach(next generation sequencing)were used to identify endophytes in grapevine stems.In the culture-dependent approach,a total of 94 isolates were recovered from 84 of 144 healthy grapevine stem fragments(colonization rate=58.3%).The study is unique as we used subsets of combined multi-gene regions to identify the endophytes to species level.Based on each multi-gene phylogenetic analysis,28 species belong to 19 genera(Acremonium,Alternaria,Arthrinium,Ascorhizoctonia,Aspergillus,Aureobasidium,Bipolaris,Botryosphaeria,Botrytis,Chaetomium,Cladosporium,Curvularia,Hypoxylon,Lasiodiplodia,Mycosphaerella,Nigrospora,Penicillium,Phoma,Scopulariopsis)were identified.A higher number of culturable fungi were obtained from 13 year-old vines,followed by eight and three yearold vines.In the culture-independent approach,a fungal richness of 59 operational taxonomic units(OTU)was detected,being highest in 13 year-old grapevines,followed by eight and three years.Even though the cultivation approach detected lower fungal richness,the results related to stem are consistent for fungal community composition and richness.Comparison of the fungal taxa identified by the two approaches resulted in an overlap of 53%of the fungal genera.Due to interspecific variability of the sequences from NGS,in many cases the OTUs(even with the highly abundant ones)were only assignable to order,family or genus level.Incorporating multi-gene phylogenies we successfully identified many of the NGS derived OTUs with poor taxonomic information in reference databases to the genus or species levels.Hence,this study signifies the importance of applying both culture-dependent and culture-independent approaches to study the fungal endophytic community composition in Vitis vinifera.This principle could also be applied to other host species and ecosystem level studies.

Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches

This study is unique as it compares traditional and high-resolution culture-independent approaches using the same set of samples to study the saprotrophic fungi on Vitis vinifera.We identified the saprotrophic communities of table grape(Red Globe)and wine grape(Carbanate Gernischet)in China using both traditional and culture-independent techniques.The traditional approach used direct observations based on morphology,single spore isolation and phylogenetic analysis yielding 45 taxa which 19 were commonly detected in both cultivars.The same set of samples were then used for Illumina sequencing which analyzed ITS1 sequence data and detected 226 fungal OTUs,of which 176 and 189 belong to the cultivars Carbanate Gernischet and Red Globe,respectively.There were 139 OTUs shared between the two V.vinifera cultivars and 37 and 50 OTUs were specific to Carbanate Gernischet and Red Globe cultivars respectively.In the Carbanate Gernischet cultivar,Ascomycota accounted for 77%of the OTUs and in Red Globe,almost all sequenced were Ascomycota.The fungal taxa overlap at the genus and species level between the traditional and culture-independent approach was relatively low.In the traditional approach we were able to identify the taxa to species level,while in the culture-independent method we were frequently able to identify the taxa to family or genus level.This is remarkable as we used the same set of samples collected in China for both approaches.We recommend the use of traditional techniques to accurately identify taxa.Culture-independent method can be used to get a better understanding about the organisms that are present in a host in its natural environment.We identified primary and secondary plant pathogens and endophytes in the saprotrophic fungal communities,which support previous observations,that dead plant material in grape vineyards can be the primary sources of disease.Finally,based on present and previous findings,we provide a worldwide checklist of 905 fungal taxa on Vitis species,which includes their mode of life and distribution.

Fungal diversity notes 1151-1276:taxonomic and phylogenetic contributions on genera and species of fungal taxa

Fungal diversity notes is one of the important journal series of fungal taxonomy that provide detailed descriptions and illustrations of new fungal taxa,as well as providing new information of fungal taxa worldwide.This article is the 11th contribution to the fungal diversity notes series,in which 126 taxa distributed in two phyla,six classes,24 orders and 55 families are described and illustrated.Taxa in this study were mainly collected from Italy by Erio Camporesi and also collected from China,India and Thailand,as well as in some other European,North American and South American countries.Taxa described in the present study include two new families,12 new genera,82 new species,five new combinations and 25 new records on new hosts and new geographical distributions as well as sexual-asexual reports.The two new families are Eriomycetaceae(Dothideomycetes,family incertae sedis)and Fasciatisporaceae(Xylariales,Sordariomycetes).The twelve new genera comprise Bhagirathimyces(Phaeosphaeriaceae),Camporesiomyces(Tubeufiaceae),Eriocamporesia(Cryphonectriaceae),Eriomyces(Eriomycetaceae),Neomonodictys(Pleurotheciaceae),Paraloratospora(Phaeosphaeriaceae),Paramonodictys(Parabambusicolaceae),Pseudoconlarium(Diaporthomycetidae,genus incertae sedis),Pseudomurilentithecium(Lentitheciaceae),Setoapiospora(Muyocopronaceae),Srinivasanomyces(Vibrisseaceae)and Xenoanthostomella(Xylariales,genera incertae sedis).The 82 new species comprise Acremonium chiangraiense,Adustochaete nivea,Angustimassarina camporesii,Bhagirathimyces himalayensis,Brunneoclavispora camporesii,Camarosporidiella camporesii,Camporesiomyces mali,Camposporium appendiculatum,Camposporium multiseptatum,Camposporium septatum,Canalisporium aquaticium,Clonostachys eriocamporesiana,Clonostachys eriocamporesii,Colletotrichum hederiicola,Coniochaeta vineae,Conioscypha verrucosa,Cortinarius ainsworthii,Cortinarius aurae,Cortinarius britannicus,Cortinarius heatherae,Cortinarius scoticus,Cortinarius subsaniosus,Cytospora fusispora,Cytospora rosigena,Diaporthe camporesii,Diaporthe nigra,Diatrypella yunnanensis,Dictyosporium muriformis,Didymella camporesii,Diutina bernali,Diutina sipiczkii,Eriocamporesia aurantia,Eriomyces heveae,Ernakulamia tanakae,Falciformispora uttaraditensis,Fasciatispora cocoes,Foliophoma camporesii,Fuscostagonospora camporesii,Helvella subtinta,Kalmusia erioi,Keissleriella camporesiana,Keissleriella camporesii,Lanspora cylindrospora,Loratospora arezzoensis,Mariannaea atlantica,Melanographium phoenicis,Montagnula camporesii,Neodidymelliopsis camporesii,Neokalmusia kunmingensis,Neoleptosporella camporesiana,Neomonodictys muriformis,Neomyrmecridium guizhouense,Neosetophoma camporesii,Paraloratospora camporesii,Paramonodictys solitarius,Periconia palmicola,Plenodomus triseptatus,Pseudocamarosporium camporesii,Pseudocercospora maetaengensis,Pseudochaetosphaeronema kunmingense,Pseudoconlarium punctiforme,Pseudodactylaria camporesiana,Pseudomurilentithecium camporesii,Pseudotetraploa rajmachiensis,Pseudotruncatella camporesii,Rhexocercosporidium senecionis,Rhytidhysteron camporesii,Rhytidhysteron erioi,Septoriella camporesii,Setoapiospora thailandica,Srinivasanomyces kangrensis,Tetraploa dwibahubeeja,Tetraploa pseudoaristata,Tetraploa thrayabahubeeja,Torula camporesii,Tremateia camporesii,Tremateia lamiacearum,Uzbekistanica pruni,Verruconis mangrovei,Wilcoxina verruculosa,Xenoanthostomella chromolaenae and Xenodidymella camporesii.The five new combinations are Camporesiomyces patagoniensis,Camporesiomyces vaccinia,Camposporium lycopodiellae,Paraloratospora gahniae and Rhexocercosporidium microsporum.The 22 new records on host and geographical distribution comprise Arthrinium marii,Ascochyta medicaginicola,Ascochyta pisi,Astrocystis bambusicola,Camposporium pellucidum,Dendryphiella phitsanulokensis,Diaporthe foeniculina,Didymella macrostoma,Diplodia mutila,Diplodia seriata,Heterosphaeria patella,Hysterobrevium constrictum,Neodidymelliopsis ranunculi,Neovaginatispora fuckelii,Nothophoma quercina,Occultibambusa bambusae,Phaeosphaeria chinensis,Pseudopestalotiopsis theae,Pyxine berteriana,Tetraploa sasicola,Torula gaodangensis and Wojnowiciella dactylidis.In addition,the sexual morphs of Dissoconium eucalypti and Phaeosphaeriopsis pseudoagavacearum are reported from Laurus nobilis and Yucca gloriosa in Italy,respectively.The holomorph of Diaporthe cynaroidis is also reported for the first time.

Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests

Fungi play vital roles in the decomposition of deadwood due to their secretion of various enzymes that break down plant cell-wall complexes.The compositions of woodinhabiting fungal(WIF)communities change over the course of the decomposition process as the remaining mass of wood decreases and both abiotic and biotic conditions of the wood significantly change.It is currently not resolved which substrate-related factors govern these changes in WIF communities and whether such changes influence the deadwood decomposition rate.Here we report a study on fungal richness and community structure in deadwood of Norway spruce and European beech in temperate forest ecosystems using 454 pyrosequencing.Our aims were to disentangle the factors that correspond to WIF community composition and to investigate the links between fungal richness,taxonomically-resolved fungal identity,and microbial-mediated ecosystem functions and processes by analyzing physico-chemical wood properties,lignin-modifying enzyme activities and wood decomposition rates.Unlike fungal richness,we found significant differences in community structure between deadwood of different tree species.The composition of WIF communities was related to the physico-chemical properties of the deadwood substrates.Decomposition rates and the activities of ligninmodifying enzymes were controlled by the succession of the fungal communities and competition scenarios rather than fungal OTU richness.Our results provide further insights into links between fungal community structure and microbialmediated ecosystem functions and processes.

亚高山森林倒木碳氮磷化学计量特征随林窗位置的变化

森林林窗对太阳辐射和降水(主要是降雨和降雪)的再分配可造成林窗内外微环境条件的异质性。本研究旨在通过改变微环境,测试林窗对倒木碳(C)、氮(N)和磷(P)化学计量比的影响。在青藏高原东部的亚高山森林中,将I-V腐解等级的岷江冷杉(Abies faxoniana)倒木分别置于林窗中心(GC)、林窗边缘(GE)和郁闭林下(CC)进行原位培养,分别于2013-2016年8月测定了腐烂树皮、边材和心材的C、N、P含量。研究结果表明,树皮N浓度从CC到GC呈下降趋势,而边材和心材则表现出相反的趋势。此外,边材和心材IV、V腐解等级的C/N从CC到GC呈下降趋势,心材V腐解等级的N/P从CC到GC呈增加趋势,这表明森林林窗对高度腐解等级倒木的C/N/P化学计量比有强烈影响。简而言之,高度腐烂的倒木更容易受到微环境的影响,必要时应适当调整郁闭林下或林窗中心的高度腐烂的倒木比例。

Fungal community succession on decomposing leaf litter across five phylogenetically related tree species in a subtropical forest

Fungi are an essential component of the ecosystem.They play an integral role in the decomposition of leaf litter and return nutrients to the ecosystem through nutrient cycling.They are considered as the“key players”in leaf litter decomposition,because of their ability to produce a wide range of extracellular enzymes.Time-related changes of fungal communities during leaf litter decomposition have been relatively well-investigated.However,it has not been established how the tree species,tree phylogeny,and leaf litter chemistry influence fungal communities during decomposition.Using direct observations and a culturing approach,this study compiles fungi found in freshly collected leaf litter from five phylogenetically related,native tree species in Taiwan:Celtis formosana(CF),Ficus ampelas(FA),Ficus septica(FS),Macaranga tanarius(MT),and Morus australis(MA).We investigated(i)the effects of tree species(including tree phylogeny)and leaf litter chemistry on fungal community succession,and(ii)specific patterns of fungal succession(including diversity and taxonomic community assembly)on decomposing leaf litter across the selected tree species.We hypothesized that host species and leaf litter chemistry significantly affect fungal community succession.A total of 1325 leaves(CF:275,FA:275,FS:275,MT:275 and MA:225)were collected and 236 fungal taxa were recorded(CF:48,FA:46,FS:64,MT:42 and MA:36).Tree species relationships had variable associations on the fungal communities,as even closely related tree species had strongly differing communities during decomposition.A high number of species were unique to a single tree species and may indicate‘host-specificity’to a particular leaf litter.The overlap of microfungal species in pair wise comparisons of tree species was low(7–16%),and only 1–2%of microfungal species were observed in leaves of all tree species.The percentage of occurrences of fungal communities using Hierarchical Cluster Analyses(HCA)showed that there were at least four succession stages in each tree species during decomposition.Fungal diversity increased at the beginning of each tree species leaf decay,reached peaks,and declined at the final stages.Overall,our findings demonstrate that tree species and leaf litter chemistry are important variables in determining fungal diversity and community composition in leaf litter.Referring to the establishment of fungal discoveries from this experimental design,two new families,two new genera,40 new species and 56 new host records were reported.This study provides a host-fungus database for future studies on these hosts and increases the knowledge of fungal diversity in leaf litter.

Positive intercropping effects on biomass production are species-specific and involve rhizosphere enzyme activities: Evidence from a field study

Less attention has been given to soil enzymes that contribute to beneficial rhizosphere interactions in intercropping systems.Therefore,we performed a field experiment by growing faba bean,lupine,and maize in mono and mixed cultures in a moderately fertile soil.We measured shoot biomass and the kinetic parameters(maximal velocity(V max)and Michaelis-constant(K m))of three key enzymes in the rhizosphere:Leucine-aminopeptidase(LAP),β-1,4-N-acetylglucosaminidase(NAG),and phosphomonoesterase(PHO).Faba bean benefitted in mixed cultures by greater shoot biomass production with both maize and lupine compared to its expected biomass in monoculture.Next,LAP and NAG kinetic parameters were less responsive to mono and mixed cultures across the crop species.In contrast,both the V max and K m values of PHO increased in the faba bean rhizosphere when grown in mixed cultures with maize and lupine.A positive relative interaction index for shoot P and N uptake for faba bean showed its net facilitative interactions in the mixed cultures.Overall,these results suggest that over-productivity in intercropping is crop-specific and the positive intercropping effects could be modulated by P availability.We argue that the enzyme activities involved in nutrient cycling should be incorporated in further research.

Taxonomic and phylogenetic contributions to fungi associated with the invasive weed Chromolaena odorata (Siam weed)

This article provides morphological descriptions and illustrations of microfungi associated with the invasive weed,Chro-molaena odorata,which were mainly collected in northern Thailand.Seventy-seven taxa distributed in ten orders,23 families(of which Neomassarinaceae is new),12 new genera(Chromolaenicola,Chromolaenomyces,Longiappendispora,Pseudocapulatispora,Murichromolaenicola,Neoophiobolus,Paraleptospora,Pseudoroussoella,Pseudostaurosphaeria,Pseudothyridariella,Setoarthopyrenia,Xenoroussoella),47 new species(Aplosporella chromolaenae,Arthrinium chromolae-nae,Chromolaenicola chiangraiensis,C.lampangensis,C.nanensis,C.thailandensis,Chromolaenomyces appendiculatus,Diaporthe chromolaenae,Didymella chromolaenae,Dyfrolomyces chromolaenae,Leptospora chromolaenae,L.phraeana,Longiappendispora chromolaenae,Memnoniella chromolaenae,Montagnula chiangraiensis,M.chromolaenae,M.chromo-laenicola,M.thailandica,Murichromolaenicola chiangraiensis,M.chromolaenae,Muyocopron chromolaenae,M.chromo-laenicola,Neomassarina chromolaenae,Neoophiobolus chromolaenae,Neopyrenochaeta chiangraiensis,N.chromolaenae,N.thailandica,N.triseptatispora,Nigrograna chromolaenae,Nothophoma chromolaenae,Paraleptospora chromolaenae,P.chromolaenicola,Patellaria chromolaenae,Pseudocapulatispora longiappendiculata,Pseudoroussoella chromolaenae,Pseudostaurosphaeria chromolaenae,P.chromolaenicola,Pseudothyridariella chromolaenae,Pyrenochaetopsis chromolae-nae,Rhytidhysteron chromolaenae,Setoarthopyrenia chromolaenae,Sphaeropsis chromolaenicola,Tremateia chiangraiensis,T.chromolaenae,T.thailandensis,Xenoroussoella triseptata,Yunnanensis chromolaenae),12 new host records,three new taxonomic combinations(Chromolaenicola siamensis,Pseudoroussoella elaeicola,Pseudothyridariella mahakashae),and two reference specimens(Torula chromolaenae,T.fici)are described and illustrated.Unlike some other hosts,e.g.bamboo(Poaceae)and Pandanaceae,the dominant group of fungi on Siam weed were Dothideomycetes.Only 15 species previously recorded from northern Thailand were found in this study.Most of the taxa are likely to have jumped hosts from surrounding plants and are unlikely to be a specialist to Siam weed.Most fungal families found on Siam weed had divergence estimates with stem ages in the Cretaceous,which coincided with the expected origin of the host family(Asteraceae).This further indicates that the species have jumped hosts,as it is unlikely that the taxa on the alien Siam weed came from the Americas with its host.They may,however,have jumped from other Asteraceae hosts.In a preliminary screening 40(65%)of the 62 species tested showed antimicrobial activity and thus,the fungi associated with C.odorata may be promising sources of novel bioactive compound discovery.We provide a checklist of fungi associated with C.odorata based on the USDA Systematic Mycology and Microbiology Laboratory(SMML)database,relevant literature and our study.In total,130 taxa(116 identified and 14 unidentified species)are distributed in 20 orders,48 families and 85 genera.Pseudocercospora is the most commonly encountered genus on Siam weed.

Can we use environmental DNA as holotypes?

The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community.The idea of using intracellular DNA("mgDNA")from environmental samples as holotypes seems at face value,to be a good idea,considering the expansion of knowledge among these‘dark taxa’or‘dark matter fungi’that it could provide(i.e.sequence based taxa without physical specimens and formal nomenclature).However,the limitations of using mgDNA as holotypes needs careful thought,i.e.can we use a short mgDNA fragment,which may contain a small amount of genetic information,to allow discrimination between species?What is the point and are the potential problems of giving valid scientific names to mgDNA?Numerous mycologists and taxonomists,who have many years of experience working on the taxonomy and phylogeny of different groups of fungi,are concerned about the consequences of providing valid names to mgDNA.There has been much debate,through several publications on the considerable problems of using mgDNA as holotypes.The proponents have tried to debate the virtues of using mgDNA as holotypes.Those against have shown that identification to species using mgDNA does not work in many fungal groups,while those for have shown cases where species can be identified with mgDNA.Different disciplines have different reasons and opinions for using mgDNA as holotypes,however even groups of the same disciplines have dissimilar ideas.In this paper we explore the use of mgDNA as holotypes.We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences.In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa,but relate the issues to fungal taxonomy.In fact we show the value of using sequence data from these approaches,in dealing with the discovery of already named taxa,taxa numbers and ecological roles.We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes.The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed.We provide evidence from case studies on Botryosphaeria,Colletotrichum,Penicillium and Xylaria.The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing.We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species.If this approach adopted,it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes.We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.