Metabarcoding of soil environmental DNA to estimate plant diversity globally

IntroductionTraditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. MethodsWe sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. ResultsLarge-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. DiscussioneDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

Global diversity and distribution of nitrogen-fixing bacteria in the soil

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

Orhideede mükoriisa seenekoosluste ajalised ja ruumilised mustrid metsa ja niidu ökosüsteemides

Väitekirja elektrooniline versioon ei sisalda publikatsiooneÜks liigirikkamaid õistaimede sugukondi on orhideelised ehk käpalised, mille liigid moodustavad tihedaid seoseid nii putuktolmeldajate kui ka seenjuurt moodustavate seentega. Orhideede mükoriisa erineb teistest mükoriisatüüpidest nii anatoomiliselt, seentaksonite poolest kui ka funktsionaalselt. Käpalised on seotud mükoriisa seentega alates seemnete idanemise faasist, kuna nende seemned on tolmpeened ning ilma idanemiseks piisavalt vajalike toitaineteta. Samas jäävad mükoriisa seened mängima olulist rolli ka hiljem, kui orhideedel arenevad rohelised lehed ja fotosünteesivõime. Arvatavasti aga muutub seensümbiotide esinemine ning kooslus täiskasvanud orhideede juurtes vegetatsiooniperioodi vältel. Tavaliselt on rohelised, s.o fotosünteesivad orhideed seotud mullas leiduvate saproobidega sugukondadest Tulasnellaceae ja Ceratobasidiaceae ning seltsist Sebacinales. Nimetatud saproobide ökoloogiat ning esinemist mullas on seni vähe uuritud. Antud doktoritöö käigus uuriti fotosünteesivate orhideeliikide mükoriisa seenekoosluste ajalisi ja ruumilisi mustreid. Töö eesmärgiks oli välja selgitada, 1) kuidas muutuvad ühe vegetatsiooniperioodi vältel täiskasvanud orhideedega seotud seensümbiontide kooslused, 2) kas seensümbiontide kooslused on mõjutatud kasvukohatüübist, 3) kas seensümbiontide rohkus on mõjutatud orhidee lähedusest ning 4) millised on nende seenekoosluste ruumilised mustrid. Lisaks oli eesmärgiks arendada seente globaalsel geenijärjestustel põhineva määraja UNITE referentsandmebaasi. Doktoritöö peamisteks tulemusteks on, et orhideede mükoriisaseente kooslused on esmalt mõjutatud orhideeliigist ning seejärel kasvukeskkonnast ning orhidee arenguetapist. Loopealsetel on orhideede mükoriisaseened mullas levinud juhuslikult ning üldjuhul ei mõjuta nende seente arvukust mullas kaugus peremeestaimest. Andmebaasi täiendamisel leiti, et avalikes andmebaasides esineb mitmeid orhideede mükoriisaseente DNA järjestusi, mis on ebakvaliteetsed ning mille kohta puuduvad metaandmed.Orchids represent one of the largest plant families and display tight associations with pollinators and mycorrhizal fungi. Orchid mycorrhizal (OrM) symbiosis is unique anatomically, taxonomically as well as functionally. Mycorrhizal fungi play a vital role for the orchids during their germination by providing essential nutrients to the dust-like orchid seeds that are almost devoid of their own food reserves. Even after orchids have developed green leaves and start photosynthesizing, their roots remain colonized by mycorrhizal fungi. However, the abundance of fungal colonization as well as the fungal community composition presumably change in the roots of the mature orchids during the vegetation period. Typically, photosynthetic, autotrophic orchids associate with saprotrophic fungi from the Ceratobasidiaceae, Tulasnellaceae and Sebacinales. So far, the distribution and ecological requirements of these fungi remain poorly explored. The aim of this thesis was therefore to study the temporal and spatial patterns of orchid mycorrhizal fungi in forest and grassland ecosystems. The thesis was particularly focused on 1) how the community composition of the putative OrM fungal taxa changes over the vegetation period in relation to the developmental phases of the host orchid species, 2) how the community composition of the putative OrM fungal taxa varies across different habitats as well as within the same habitat and on 3) how the richness of putative OrM fungi changes with the increasing distance from the orchid patches and 4) whether the putative OrM fungi form spatial patterns along the distance from the orchid patches. In addition, we extended annotations of publicly available OrM fungal ITS sequences. The main results of the thesis can be summarized as follows: 1) the community composition of the OrM fungi in roots was primarily host dependent and only secondarily affected by habitat and even to a lesser degree by the developmental phase and 2) in semi-natural grasslands, OrM fungi were randomly distributed and showed little evidence of a distance-dependent decline away from the adult orchids. We detected a number of insufficiently annotated OrM fungal sequences deposited in public databases, as well as sequences which suffered from low read quality and/or chimeras

Linking Soil Chemical Parameters and Fungal Diversity in Qatar

Given the vast expanse of Qatar's dryland ecosystems, agricultural productivity and soil stability is highly dependent on the diversity of soil microbiota. The soil environment is a heterogeneous habitat shaped by various components like chemical (organic matter, salinity and nutrients) and biological (fungal diversity and vegetation) properties that form multitudes of different microhabitats. Soil microbial diversity changes along environmental gradients. It is hypothesized that a "stable" microhabitat is one that is inhabited by a large diversity of established microorganisms that are best adapted to the niche. Microorganisms like fungi serve as the underlying biological drivers for biochemical processes within the soil. The key objective of this study is to evaluate the fungal diversity and abundance present within the Qatari soil using molecular-based tools and evaluate potential relationships between the identified fungal communities with chemical properties of the habitat. We found that the composition of fungi and AMF varied between different habitats around Qatar. Despite the lack of significant differences in the measured soil chemical parameters between sampled sites, it is evident that AMF species are more abundant than compared to that of other fungal species in most of the study sites; thus, suggesting that other factors like land use may also be an essential component explaining the variation in fungal communities

Impacts of elevated atmospheric CO2 on arbuscular mycorrhizal fungi and their role in moderating plant allometric partitioning

Elevated atmospheric CO2 concentration (eCO2) effects on plants depend on several factors including plant photosynthetic physiology (e.g. C3, C4), soil nutrient availability and plants’ co-evolved soil-dwelling fungal symbionts, namely arbuscular mycorrhizal (AM) fungi. Complicated interactions among these components will determine the outcomes for plants. Therefore, clearer understanding is needed of how plant growth and nutrient uptake, along with root-colonising AM fungal communities, are simultaneously impacted by eCO2. We conducted a factorial growth chamber experiment with a C3 and a C4 grass species (± AM fungi and ± eCO2). We found that eCO2 increased plant biomass allocation towards the roots, but only in plants without AM fungi, potentially associated with an eCO2-driven increase in plant nutrient requirements. Furthermore, our data suggest a difference in the identities of root-colonising fungal taxa between ambient CO2 and eCO2 treatments, particularly in the C4 grass species, although this was not statistically significant. As AM fungi are ubiquitous partners of grasses, their response to increasing atmospheric CO2 is likely to have important consequences for how grassland ecosystems respond to global change