Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil ...microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations, and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria, and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen, and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.
Abstract
Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related ...to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.
Being highly sensitive to ecological variations, symbiotic associations should inherently have a limited occurrence in nature. To circumvent this sensitivity and reach their universal distribution, ...symbioses used three strategies during their evolution, which all generated high biodiversity levels: (i) specialization to a specific environment, (ii) protection of one partner via its internalization into the other, (iii) frequent partner exchange. Mycorrhizal associations follow the 3rd strategy, but also present traits of internalization. As most ancient type, arbuscular mycorrhiza (AM) formed by a monophyletic fungal group with reduced species richness did constantly support the mineral nutrition of terrestrial plants and enabled their ecological radiation and actual biodiversity level. In contrast ectomycorrhiza (EM) evolved later and independently within different taxa of fungi able to degrade complex organic plant residues, and the diversity levels of EM fungal and tree partners are balanced. Despite their different origins and diversity levels, AM and EM fungi display similar patterns of diversity dynamics in ecosystems. At each time or succession interval, a few dominant and many rare fungi are recruited by plants roots from a wide reservoir of propagules. However, the dominant fungal partners are frequently replaced in relation to changes in the vegetation or ecological conditions. While the initial establishment of AM and EM fungal communities corresponds to a neutral recruitment, their further succession is rather driven by niche differentiation dynamics.
Wood-inhabiting fungi have essential roles in the regulation of carbon stocks and nutrient cycling in forest ecosystems. However, knowledge pertaining to wood-inhabiting fungi is only fragmentary and ...controversial. Here we established a large-scale deadwood experiment with 11 tree species to investigate diversity and tree species preferences of wood-inhabiting fungi using next-generation sequencing. Our results contradict existing knowledge based on sporocarp surveys and challenge current views on their distribution and diversity in temperate forests. Analyzing α-, β- and γ-diversity, we show that diverse fungi colonize deadwood at different spatial scales. Specifically, coniferous species have higher α- and γ-diversity than the majority of analyzed broadleaf species, but two broadleaf species showed the highest β-diversity. Surprisingly, we found nonrandom co-occurrence (P<0.001) and strong tree species preferences of wood-inhabiting fungi, especially in broadleaf trees (P<0.01). Our results indicate that the saprotrophic fungal community is more specific to tree species than previously thought.
To understand the fine‐scale effects of changes in nutrient availability on eukaryotic soil microorganisms communities, a multiple barcoding approach was used to analyse soil samples from four ...different treatments in a long‐term fertilization experiment. We performed PCR amplification on soil DNA with primer pairs specifically targeting the 18S rRNA genes of all eukaryotes and three protist groups (Cercozoa, Chrysophyceae‐Synurophyceae and Kinetoplastida) as well as the ITS gene of fungi and the 23S plastid rRNA gene of photoautotrophic microorganisms. Amplicons were pyrosequenced, and a total of 88 706 quality filtered reads were clustered into 1232 operational taxonomic units (OTU) across the six data sets. Comparisons of the taxonomic coverage achieved based on overlapping assignment of OTUs revealed that half of the eukaryotic taxa identified were missed by the universal eukaryotic barcoding marker. There were only little differences in OTU richness observed between organic‐ (farmyard manure), mineral‐ and nonfertilized soils. However, the community compositions appeared to be strongly structured by organic fertilization in all data sets other than that generated using the universal eukaryotic 18S rRNA gene primers, whereas mineral fertilization had only a minor effect. In addition, a co‐occurrence based network analysis revealed complex potential interaction patterns between OTUs from different trophic levels, for example between fungivorous flagellates and fungi. Our results demonstrate that changes in pH, moisture and organic nutrients availability caused shifts in the composition of eukaryotic microbial communities at multiple trophic levels.
The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in ...the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche-partitioning between them is limited. Here, a microcosm experiment was performed to trace the flow of detritusphere C from substrate analogs (glucose, cellulose) and plant biomass amendments (maize leaves, roots) in an agricultural soil. Carbon flow was traced by rRNA stable isotope probing and amplicon sequencing across three microbial kingdoms. Distinct lineages within the
as well as
were identified as important primary substrate consumers. A dynamic succession of primary consumers was observed especially in the cellulose treatments, but also in plant amendments over time. While intra-kingdom niche partitioning was clearly observed, distinct bacterial and fungal energy channels were not apparent. Furthermore, while the diversity of primary substrate consumers did not notably increase with substrate complexity, consumer succession and secondary trophic links to bacterivorous and fungivorous microbes resulted in increased food web complexity in the more recalcitrant substrates. This suggests that rather than substrate-defined energy channels, consumer succession as well as intra- and inter-kingdom cross-feeding should be considered as mechanisms supporting food web complexity in the detritusphere.
Experiments showed that biodiversity increases grassland productivity and nutrient exploitation, potentially reducing fertiliser needs. Enhancing biodiversity could improve P-use efficiency of ...grasslands, which is beneficial given that rock-derived P fertilisers are expected to become scarce in the future. Here, we show in a biodiversity experiment that more diverse plant communities were able to exploit P resources more completely than less diverse ones. In the agricultural grasslands that we studied, management effects either overruled or modified the driving role of plant diversity observed in the biodiversity experiment. Nevertheless, we show that greater above- (plants) and belowground (mycorrhizal fungi) biodiversity contributed to tightening the P cycle in agricultural grasslands, as reduced management intensity and the associated increased biodiversity fostered the exploitation of P resources. Our results demonstrate that promoting a high above- and belowground biodiversity has ecological (biodiversity protection) and economical (fertiliser savings) benefits. Such win-win situations for farmers and biodiversity are crucial to convince farmers of the benefits of biodiversity and thus counteract global biodiversity loss.
Decomposition by microorganisms of plastics in soils is almost unexplored despite the fact that the majority of plastics released into the environment end up in soils. Here, we investigate the ...decomposition process and microbiome of one of the most promising biobased and biodegradable plastics, poly(butylene succinate-co-adipate) (PBSA), under field soil conditions under both ambient and future predicted climates (for the time between 2070 and 2100). We show that the gravimetric and molar mass of PBSA is already largely reduced (28–33%) after 328 days under both climates. We provide novel information on the PBSA microbiome encompassing the three domains of life: Archaea, Bacteria, and Eukarya (fungi). We show that PBSA begins to decompose after the increase in relative abundances of aquatic fungi (Tetracladium spp.) and nitrogen-fixing bacteria. The PBSA microbiome is distinct from that of surrounding soils, suggesting that PBSA serves as a new ecological habitat. We conclude that the microbial decomposition process of PBSA in soil is more complex than previously thought by involving interkingdom relationships, especially between bacteria and fungi.
Tracking, targeting, and conserving soil biodiversity Guerra, Carlos A; Bardgett, Richard D; Caon, Lucrezia ...
Science (American Association for the Advancement of Science),
2021-Jan-15, 2021-01-15, 20210115, Letnik:
371, Številka:
6526
Journal Article
Recenzirano
Odprti dostop
A monitoring and indicator system can inform policy
Nature conservation literature and policy instruments mainly focus on the impacts of human development and the benefits of nature conservation for ...oceans and aboveground terrestrial organisms (e.g., birds and plants) and processes (e.g., food production), but these efforts almost completely ignore the majority of terrestrial biodiversity that is unseen and living in the soil (
1
). Little is known about the conservation status of most soil organisms and the effects of nature conservation policies on soil systems. Yet like “canaries in the coal mine,” when soil organisms begin to disappear, ecosystems will soon start to underperform, potentially hindering their vital functions for humankind. Soil biodiversity and its ecosystem functions thus require explicit consideration when establishing nature protection priorities and policies and when designing new conservation areas. To inform such efforts, we lay out a global soil biodiversity and ecosystem function monitoring framework to be considered in the context of the post-2020 discussions of the Convention on Biological Diversity (CBD). To support this framework, we suggest a suite of soil ecological indicators based on essential biodiversity variables (EBVs) (
2
) (see the figure and table S3) that directly link to current global targets such as the ones established under the CBD, the Sustainable Development Goals (SDGs), and the Paris Agreement (table S1).
This article provides morphological descriptions and illustrations of microfungi associated with the invasive weed,
Chromolaena 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 chromolaenae
,
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. chromolaenicola
,
M. thailandica
,
Murichromolaenicola chiangraiensis
,
M. chromolaenae
,
Muyocopron chromolaenae
,
M. chromolaenicola
,
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 chromolaenae
,
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.
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