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Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 32523

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Dr. Tim J. Dumonceaux

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Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2, Canada
Interests: molecular diagnostics; agricultural microbiology; microbial communities; biofuels; plant pathology
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Special Issue Information

Dear Colleagues,

Terrestrial microbial ecosystems provide a wide array of ecosystem services related to organic matter decomposition, soil formation, nutrient fluxes, and elemental cycling. Management intensity, especially the influence of anthropogenic inputs, impacts microbial ecosystems to varying degrees. Moreover, the effects of climate change, including extreme weather events as well as changes in the geographic distribution of plants and animals, are expected to impact microbial communities. Determining the composition of microbial ecosystems and how they respond to such perturbations is a critical step to fully understand the impacts of anthropogenic influences on forest and agricultural systems that provide essential provisioning, supporting and regulating ecosystem services to humans. Recent dramatic improvements in the ability to generate and analyze DNA sequence data (metagenomics) have provided the means to begin answering these critical questions. In this Special Issue, we aim to bring together studies from a wide array of scientists studying plant- and soil-associated microbial ecosystems in both agricultural and forest environments. We encourage submissions that examine the influence of perturbations on the ecosystem services provided by microbial communities, as well as the effects of changes in pest distribution on microbial communities. Studies that describe novel methods to address these questions are also welcomed.

Dr. Tim J. Dumonceaux
Guest Editor

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Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

Biodiversity
Ecosystem Services
Soil Microbial Ecosystems
Metagenomics
Climate Change

Related Special Issue

Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0 in Microorganisms (12 articles)

Published Papers (11 papers)

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Research

11 pages, 2270 KiB

Open AccessArticle

Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

by Aleksei O. Zverev, Arina A. Kichko, Aleksandr G. Pinaev, Nikolay A. Provorov and Evgeny E. Andronov

Microorganisms 2021, 9(11), 2339; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112339 - 12 Nov 2021

Cited by 11 | Viewed by 2266

Abstract

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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20 pages, 6611 KiB

Open AccessArticle

Soil Layers Matter: Vertical Stratification of Root-Associated Fungal Assemblages in Temperate Forests Reveals Differences in Habitat Colonization

by Anis Mahmud Khokon, Dominik Schneider, Rolf Daniel and Andrea Polle

Microorganisms 2021, 9(10), 2131; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9102131 - 11 Oct 2021

Cited by 7 | Viewed by 2221

Abstract

Ectomycorrhizal and saprotrophic fungi play pivotal roles in ecosystem functioning. Here, we studied the vertical differentiation of root-associated fungi (RAF) in temperate forests. We analysed RAF assemblages in the organic and mineral soil from 150 experimental forest plots across three biogeographic regions spanning a distance of about 800 km. Saprotrophic RAF showed the highest richness in organic and symbiotrophic RAF in mineral soil. Symbiotrophic RAF exhibited higher relative abundances than saprotrophic fungi in both soil layers. Beta-diversity of RAF was mainly due to turnover between organic and mineral soil and showed regional differences for symbiotrophic and saprotrophic fungi. Regional differences were also found for different phylogenetic levels, i.e., fungal orders and indicator species in the organic and mineral soil, supporting that habitat conditions strongly influence differentiation of RAF assemblages. Important exceptions were fungal orders that occurred irrespective of the habitat conditions in distinct soil layers across the biogeographic gradient: Russulales and Cantharellales (ectomycorrhizal fungi) were enriched in RAF assemblages in mineral soil, whereas saprotrophic Polyporales and Sordariales and ectomycorrhizal Boletales were enriched in RAF assemblages in the organic layer. These results underpin a phylogenetic signature for niche partitioning at the rank of fungal orders and suggest that RAF assembly entails two strategies encompassing flexible and territorial habitat colonization by different fungal taxa. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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20 pages, 4124 KiB

Open AccessArticle

Does Organic Farming Increase Raspberry Quality, Aroma and Beneficial Bacterial Biodiversity?

by Daniela Sangiorgio, Antonio Cellini, Francesco Spinelli, Brian Farneti, Iuliia Khomenko, Enrico Muzzi, Stefano Savioli, Chiara Pastore, María Teresa Rodriguez-Estrada and Irene Donati

Microorganisms 2021, 9(8), 1617; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081617 - 29 Jul 2021

Cited by 16 | Viewed by 3180

Abstract

Plant-associated microbes can shape plant phenotype, performance, and productivity. Cultivation methods can influence the plant microbiome structure and differences observed in the nutritional quality of differently grown fruits might be due to variations in the microbiome taxonomic and functional composition. Here, the influence of organic and integrated pest management (IPM) cultivation on quality, aroma and microbiome of raspberry (Rubus idaeus L.) fruits was evaluated. Differences in the fruit microbiome of organic and IPM raspberry were examined by next-generation sequencing and bacterial isolates characterization to highlight the potential contribution of the resident-microflora to fruit characteristics and aroma. The cultivation method strongly influenced fruit nutraceutical traits, aroma and epiphytic bacterial biocoenosis. Organic cultivation resulted in smaller fruits with a higher anthocyanidins content and lower titratable acidity content in comparison to IPM berries. Management practices also influenced the amounts of acids, ketones, aldehydes and monoterpenes, emitted by fruits. Our results suggest that the effects on fruit quality could be related to differences in the population of Gluconobacter, Sphingomonas, Rosenbergiella, Brevibacillus and Methylobacterium on fruit. Finally, changes in fruit aroma can be partly explained by volatile organic compounds (VOCs) emitted by key bacterial genera characterizing organic and IPM raspberry fruits. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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15 pages, 3239 KiB

Open AccessArticle

First Evidence That Nematode Communities in Deadwood Are Related to Tree Species Identity and to Co-Occurring Fungi and Prokaryotes

by Julia Moll, Friederike Roy, Claus Bässler, Jacob Heilmann-Clausen, Martin Hofrichter, Harald Kellner, Doris Krabel, Jan Henrik Schmidt, François Buscot and Björn Hoppe

Microorganisms 2021, 9(7), 1454; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071454 - 06 Jul 2021

Cited by 8 | Viewed by 2943

Abstract

Nematodes represent a diverse and ubiquitous group of metazoans in terrestrial environments. They feed on bacteria, fungi, plants, other nematodes or parasitize a variety of animals and hence may be considered as active members of many food webs. Deadwood is a structural component of forest ecosystems which harbors many niches for diverse biota. As fungi and bacteria are among the most prominent decomposing colonizers of deadwood, we anticipated frequent and diverse nematode populations to co-occur in such ecosystems. However, knowledge about their ability to colonize this habitat is still limited. We applied DNA-based amplicon sequencing (metabarcoding) of the 18S rRNA gene to analyze nematode communities in sapwood and heartwood of decaying logs from 13 different tree species. We identified 247 nematode ASVs (amplicon sequence variants) from 27 families. Most of these identified families represent bacterial and fungal feeders. Their composition strongly depended on tree species identity in both wood compartments. While pH and water content were the only wood properties that contributed to nematodes’ distribution, co-occurring fungal and prokaryotic (bacteria and archaea) α- and β-diversities were significantly related to nematode communities. By exploring thirteen different tree species, which exhibit a broad range of wood characteristics, this study provides first and comprehensive insights into nematode diversity in deadwood of temperate forests and indicates connectivity to other wood-inhabiting organisms. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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13 pages, 3499 KiB

Open AccessArticle

Preventing Extinction of the Critically Endangered Dactylorhiza incarnata subsp. ochroleuca in Britain Using Symbiotic Seedlings for Reintroduction

by Viswambharan Sarasan, Tim Pankhurst, Kazutomo Yokoya, Sridevy Sriskandarajah and Faye McDiarmid

Microorganisms 2021, 9(7), 1421; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071421 - 30 Jun 2021

Cited by 2 | Viewed by 2749

Abstract

The yellow early marsh-orchid (Dactylorhiza incarnata subsp. ochroleuca) is critically endangered in the UK. Reintroduction of this threatened orchid to former haunts that have been restored is a long-term objective of this study. Identifying germination-specific mycorrhizal fungus lineages from closely related species is used as a method due to the extremely small number of plants left in the wild. A putative orchid mycorrhizal fungus of the family Tulasnellaceae, isolated from Dactylorhiza praetermissa, supported in vitro seed germination to produce reintroduction-ready seedlings. Reintroduced symbiotic seedlings survived over the winter months in the flooded reintroduction site (RS). The comparative soil analysis for key nutrients before reintroduction showed that phosphorus content in the RS is very low compared to the soil collected from the wild site (WS) where the last viable population exists. On the other hand, C:N ratio in the soil at the WS and RS were not significantly different. To our knowledge, this is the first-ever report on the reintroduction of symbiotic seedlings of a threatened orchid back to the wild in the UK. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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24 pages, 2271 KiB

Open AccessArticle

Soil Microbial Indicators within Rotations and Tillage Systems

by Gevan D. Behnke, Nakian Kim, Maria C. Zabaloy, Chance W. Riggins, Sandra Rodriguez-Zas and Maria B. Villamil

Microorganisms 2021, 9(6), 1244; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061244 - 08 Jun 2021

Cited by 21 | Viewed by 2958

Abstract

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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13 pages, 843 KiB

Open AccessArticle

Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other

by Alen K. Eskov, Alexei O. Zverev and Evgeny V. Abakumov

Microorganisms 2021, 9(5), 1033; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9051033 - 11 May 2021

Cited by 10 | Viewed by 2047

Abstract

Microbial biodiversity parameters for tropical rainforests remain poorly understood. Whilst the soil microbiome accounts up to 95% of the total diversity of microorganisms in terrestrial ecosystems, the microbiome of suspended soils formed by vascular epiphytes remains completely unexplored. Samples of ground and suspended soils were collected in Cat Tien National Park, southern Vietnam. DNA extraction and sequencing were performed, and libraries of 16s rDNA gene sequences were analyzed. Alpha diversity indices of the microorganisms were the highest in the forest ground soil. In general, the microbiological diversity of all the soil types was found to be similar at the phylum level. Taxonomic composition of the bacterial communities in the suspended soils of plants from the same species are not closer than the taxonomic compositions of the communities in the suspended soils of different plant species. However, the beta diversity analysis revealed significant differences in the movement of mineral elements in terrestrial versus suspended soils. Our data showed that the suspended soils associated with vascular epiphytes were a depository of unique microbiological biodiversity. A contributing factor was the presence of large amounts of organic matter in the suspended soils—deposits collected by the epiphytes—which would have been degraded by termites if it had reached the ground. Further, the nutrient content of the suspended soils was prime for soil respiration activity and taxonomic microbial community biodiversity. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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17 pages, 19759 KiB

Open AccessArticle

The Impact of Pine Wood Nematode Infection on the Host Fungal Community

by Yi Liu, Zhao-Lei Qu, Bing Liu, Yang Ma, Jie Xu, Wen-Xiao Shen and Hui Sun

Microorganisms 2021, 9(5), 896; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9050896 - 22 Apr 2021

Cited by 11 | Viewed by 2323

Abstract

Pine wilt disease (PWD), caused by pinewood nematode (PWN) Bursaphelenchus xylophilus, is globally one of the most destructive diseases of pine forests, especially in China. However, little is known about the effect of PWD on the host microbiome. In this study, the fungal community and functional structures in the needles, roots, and soil of and around Pinus thunbergii naturally infected by PWN were investigated by using high-throughput sequencing coupled with the functional prediction (FUNGuild). The results showed that fungal richness, diversity, and evenness in the needles of diseased trees were significantly lower than those of healthy ones (p < 0.05), whereas no differences were found in the roots and soil. Principal coordinate analysis (PCoA) showed that the fungal community and functional structures significantly differed only in the needles of diseased and healthy trees, but not in the soil and roots. Functionally, the saprotrophs had a higher abundance in the needles of diseased trees, whereas symbiotrophs abundance was higher in the needles of healthy trees (linear discriminant analysis (LDA) > 2.0, p < 0.05). These results indicated that PWN infection primarily affected the fungal community and functional structures in the needles of P. thunbergii, but not the roots and soil. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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24 pages, 2842 KiB

Open AccessArticle

CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

by Matthew G. Links, Tim J. Dumonceaux, E. Luke McCarthy, Sean M. Hemmingsen, Edward Topp and Jennifer R. Town

Microorganisms 2021, 9(4), 816; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040816 - 13 Apr 2021

Cited by 6 | Viewed by 2511

Abstract

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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19 pages, 4455 KiB

Open AccessArticle

Fungal Diversity of Selected Habitat Specific Cynorkis Species (Orchidaceae) in the Central Highlands of Madagascar

by Kazutomo Yokoya, Alison S. Jacob, Lawrence W. Zettler, Jonathan P. Kendon, Manoj Menon, Jake Bell, Landy Rajaovelona and Viswambharan Sarasan

Microorganisms 2021, 9(4), 792; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040792 - 10 Apr 2021

Cited by 5 | Viewed by 2870

Abstract

About 90% of Cynorkis species are endemic to the biodiversity hotspot of Madagascar. This terrestrial habitat-specific genus received little study for fungal diversity to support conservation. We evaluated the diversity of culturable fungi of 11 species and soil characteristics from six sites spanning a >40 km radius in and along the region’s inselbergs. Peloton-forming fungi were grown in vitro from root/protocorm slices and positively identified using DNA sequencing. The fungal diversity was then correlated with soil pH, NO₃^-N, P, and K. All species harbored either putative mycorrhizal associates in the Rhizoctonia complex or Hypocreales fungi. Tulasnella Operational Taxonomic Units (OTUs) were most prevalent in all soil types while Serendipita OTUs were found in species inhabiting granite/rock outcrops in moist soil (seepage areas). Most Cynorkis species were present in soil with low NO₃^-N and P levels with diversity of mycorrhizal fungi inversely correlated to NO₃^-N levels. Of the different orchid life stages sampled, only one species (Cynorkis fastigiata) yielded putative mycorrhizal fungi from juvenile stages. As diversity of mycorrhizal fungi of Cynorkis spp. was negatively correlated with NO₃^-N, and majority of the studied taxa were found in soils with low NO₃^-N and P contents, reintroduction studies must include analysis of N and P in detail. For the first time, we showed that the assemblage of culturable fungi in the roots of habitat-specific species of Cynorkis (Orchidaceae) are intimately tied to specific soil characteristics. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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18 pages, 7880 KiB

Open AccessArticle

Relative Abundances of Species or Sequence Variants Can Be Misleading: Soil Fungal Communities as an Example

by Lukas Beule, Markus Arndt and Petr Karlovsky

Microorganisms 2021, 9(3), 589; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9030589 - 13 Mar 2021

Cited by 16 | Viewed by 5126

Abstract

Plant production systems that are more sustainable than conventional monoculture croplands are the vision of future agriculture. With numerous environmental benefits, agroforestry is among the most promising alternatives. Although soil fungi are key drivers of plant productivity and ecosystem processes, investigations of these microorganisms in temperate agroforestry systems are scarce, leaving our understanding of agricultural systems under agroforestry practice incomplete. Here, we assessed the composition and diversity of the soil fungal community as well as the frequency (relative abundance) of fungal groups in three paired temperate poplar-based alley cropping (agroforestry) and monoculture cropland systems by amplicon sequencing. Analysis of microbiomes using relative abundances of species or sequence variants obtained from amplicon sequencing ignores microbial population size, which results in several problems. For example, species stimulated by environmental parameters may appear unaffected or suppressed in amplicon counts. Therefore, we determined absolute abundances of selected fungal groups as well as total fungal population size by real-time polymerase chain reaction (PCR). Tree rows strongly affected the community composition and increased the population size and species richness of soil fungi. Furthermore, ectomycorrhiza were strongly promoted by the tree rows. We speculate that mycorrhiza improved the nutrient acquisition in unfertilized tree rows, thereby contributing to the total productivity of the system. Comparison of relative and absolute abundances revealed dramatic discrepancies, highlighting that amplicon sequencing alone cannot adequately assess population size and dynamics. The results of our study highlight the necessity of combining frequency data based on amplicon sequencing with absolute quantification. Full article

(This article belongs to the Special Issue Composition and Dynamics of Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems)

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