Mechanistic modeling indicates rapid glyphosate dissipation and sorption-driven persistence of its metabolite AMPA in soil.

Residual concentrations of glyphosate and its main transformation product aminomethylphosphonic acid (AMPA) are often observed in soils. The factors controlling their biodegradation are currently not well understood. We analyzed sorption-limited biodegradation of glyphosate and AMPA in soil with a set of microcosm experiments. A mechanistic model that accounts for equilibrium and kinetic sorption facilitated interpretation of the experimental results. Both compounds showed a biphasic dissipation with an initial fast (up to Days 7-10) and subsequent slower transformation rate, pointing to sorption-limited degradation. Glyphosate transformation was well described by considering only equilibrium sorption. Model simulations suggested that only 0.02-0.13% of total glyphosate was present in the soil solution and thus bioavailable. Glyphosate transformation was rapid in solution (time required for 50 % dissipation of the total initially added chemical [DT50 ] = 3.9 min), and, despite strong equilibrium sorption, total glyphosate in soil dissipated quickly (DT50  = 2.4 d). Aminomethylphosphonic acid dissipation kinetics could only be described when considering both equilibrium and kinetic sorption. In comparison to glyphosate, the model simulations showed that a higher proportion of total AMPA was dissolved and directly bioavailable (0.27-3.32%), but biodegradation of dissolved AMPA was slower (DT50  = 1.9 h). The model-based data interpretation suggests that kinetic sorption strongly reduces AMPA bioavailability, leading to increased AMPA persistence in soil (DT50  = 12 d). Thus, strong sorption combined with rapid degradation points to low risks of glyphosate leaching by vertical transport through soil in the absence of preferential flow. Ecotoxicological effects on soil microorganisms might be reduced. In contrast, AMPA persists, rendering these risks more likely.

Environmental response of arbuscular mycorrhizal fungi under soybean cultivation at a regional scale.

Climate change, the shortage of fertilizers and reduced land for cultivation have drawn attention to the potential aid provided by soil-borne organisms. Arbuscular mycorrhizal fungi (AMF) offer a wide range of ecosystem benefits and hence, understanding the mechanisms that control AMF occurrence and maintenance is essential for resilient crop production. We conducted a survey of 123 soybean fields located across a 75,000-km2 area of Argentina to explore AMF community composition and to quantify the impact of soil, climate, and geographical distance on these key soil organisms. First, based upon morphological identification of spores, we compiled a list of the AMF species found in the studied area and identified Acaulospora scrobiculata and Glomus fuegianum as the most frequent species. G. fuegianum abundance was negatively correlated with precipitation seasonality and positively correlated with mean annual precipitation as well as mycorrhizal colonisation of soybean roots. Second, we observed that species richness was negatively correlated with soil P availability (Bray I), clay content and mean annual precipitation. Finally, based on partitioning variation analysis, we found that AMF exhibited spatial patterning at a broad scale. Therefore, we infer that geographical distance was positively associated with spore community composition heterogeneity across the region. Nevertheless, we highlight the importance of precipitation sensitivity of frequent species, overall AMF richness and community composition, revealing a crucial challenge to forthcoming agriculture considering an expected change in global climate patterns.

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline.

One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination with bioinformatics analyses. However, focusing on environmental samples from contrasting habitats, it was not systematically evaluated (i) which analysis methods provide results that reflect reality most accurately, (ii) how the interpretations of microbial community studies are biased by different analysis methods and (iii) if the most optimal analysis workflow can be implemented in an easy-to-use pipeline. Here, we compared the performance of 16S rRNA (gene) amplicon sequencing analysis tools (i.e., Mothur, QIIME1, QIIME2, and MEGAN) using three mock datasets with known microbial community composition that differed in sequencing quality, species number and abundance distribution (i.e., even or uneven), and phylogenetic diversity (i.e., closely related or well-separated amplicon sequences). Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), suggesting that this approach is able to reflect the in situ microbial community most accurately. Further analysis of 24 environmental datasets obtained from four contrasting terrestrial and freshwater sites revealed dramatic differences in the resulting microbial community composition for all pipelines at genus level. For instance, at the investigated river water sites Sphaerotilus was only reported when using QIIME1 (8% abundance) and Agitococcus with QIIME1 or QIIME2 (2 or 3% abundance, respectively), but both genera remained undetected when analyzed with Mothur or MEGAN. Since these abundant taxa probably have implications for important biogeochemical cycles (e.g., nitrate and sulfate reduction) at these sites, their detection and semi-quantitative enumeration is crucial for valid interpretations. A high-performance computing conformant workflow was constructed to allow FAIR (Findable, Accessible, Interoperable, and Re-usable) 16S rRNA (gene) amplicon sequence analysis starting from raw sequence files, using the most optimal methods identified in our study. Our presented workflow should be considered for future studies, thereby facilitating the analysis of high-throughput 16S rRNA (gene) sequencing data substantially, while maximizing reliability and confidence in microbial community data analysis.

Metabarcoding analysis of home composts reveals distinctive fungal communities with a high number of unassigned sequences.

Home composting has been strongly advocated in the UK, Europe and North America to divert organic waste away from conventional waste processing. Despite this, little attention has been given to microbial communities and their diversity in these systems. In this study, we examined the diversity of fungal species in 10 different domestic composts by 454 tag-encoded pyrosequencing. We report the recovery of 478 different molecular operational taxonomic units (MOTUs) from the 10 composts with a mean of 176.7 ± 19.6 MOTUs per compost and a mean of 12.9 ± 3.8 unique MOTUs per sample. Microascales (17.21 %), Hypocreales (16.76 %), Sordariales (14.89 %), Eurotiales (11.25 %) and Mortierellales (7.38 %) were the dominant orders in the community, with Pseudallescheria (9.52 %), Penicillium (8.43 %), Mortierella (3.60 %) and Fusarium (3.31 %) being the most abundant genera. Fungal communities in home composts were substantially different to large-scale commercial composts, with thermophilic and thermotolerant fungi present in much lower numbers. Significantly, 46.2 % of all sequences were identified as uncultured fungi or could not be assigned above the family level, suggesting there are a high number of new genera and species in these environments still to be described.

Biodegradation of polyester polyurethane during commercial composting and analysis of associated fungal communities.

In this study the biodegradation of polyurethane (PU) during the maturation stage of a commercial composting process was investigated. PU coupons were buried in the centre and at the surface of a 10 m high compost pile. Fungal communities colonising polyester PU coupons were compared with the native compost communities using culture based and molecular techniques. Putative polyester PU degrading fungi were ubiquitous in compost and rapidly colonised the surface of polyester PU coupons with significant deterioration. As the temperature decreased, fungal diversity in the compost and on the surface of the polyester PU coupons increased and selection of fungal community on the polyester PU coupons occurs that is different from the surrounding compost.

Fungal succession in an in-vessel composting system characterized using 454 pyrosequencing.

Fungi are known to have an important role in the composting process as degraders of recalcitrant materials such as cellulose and lignin. Previous attempts to study the diversity and succession of fungi in compost systems have relied on the use of culture-dependent analyses and low-resolution DNA-fingerprinting techniques, lacking the necessary depth to analyse such a rich ecosystem. In this study, 454 pyrosequencing was used to characterize the fungal community composition at the different stages of an in-vessel composting process. A complex succession of fungi was revealed, with 251 fungal OTUs identified throughout the monitoring period. The Ascomycota were the dominant phylum (82.5% of all sequences recovered), followed by the Basidiomycota (10.4%) and the subphylum Mucoromycotina (4.9%). In the starting materials and early stages of the process, yeast species from the Saccharomycetales were abundant, while in latter stages and in the high temperature regions of the pile, fungi from the orders Eurotiales, Sordariales, Mucorales, Agaricales and Microascales were the most prominent. This study provides an improved understanding of the fungal diversity occurring during the composting of municipal solid waste, and this knowledge can lead to the development of more efficient composting practices and a better evaluation of the end-product quality.