Datathons: fostering equitability in data reuse in ecology.

Approaches to rapidly collecting global biodiversity data are increasingly important, but biodiversity blind spots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to date and formed collaborative consortia for microbiome data synthesis.

Microbiomes and glyphosate biodegradation in edaphic and aquatic environments: recent issues and trends.

Glyphosate (N-(phosphonomethyl)glycine) has emerged as the top-selling herbicide worldwide because of its versatility in controlling annual and perennial weeds and the extensive use of glyphosate-resistant crops. Concerns related to the widespread use of glyphosate and its ubiquitous presence in the environment has led to a large number of studies and reviews, which examined the toxicity and fate of glyphosate and its major metabolite, aminomethylphosphonic acid (AMPA) in the environment. Because the biological breakdown of glyphosate is most likely the main elimination process, the biodegradation of glyphosate has also been the object of abundant experimental work. Importantly, glyphosate biodegradation in aquatic and soil ecosystems is affected not only by the composition and the activity of microbial communities, but also by the physical environment. However, the interplay between microbiomes and glyphosate biodegradation in edaphic and aquatic environments has rarely been considered before. The proposed minireview aims at filling this gap. We summarize the most recent work exploring glyphosate biodegradation in natural aquatic biofilms, the biological, chemical and physical factors and processes playing on the adsorption, transport and biodegradation of glyphosate at different levels of soil organization and under different agricultural managements, and its impact on soil microbial communities.

Efecto de los cultivos de cobertura invernales sobre el microbioma del suelo: revisión sistemática de la literatura / Effect of winter cover crops on the soil microbiome: a systematic literature review

Resumen La inclusión de cultivos de cobertura invernales (CCI) en un sistema de siembra directa (SD) en reemplazo del barbecho constituye una alternativa promisoria para mejorar la salud del suelo y contribuir a la sustentabilidad ambiental de los sistemas agrícolas. Esta revisión ofrece un panorama integral de los efectos sobre el microbioma del suelo que tiene la introducción de CCI en rotación con cultivos de verano en sistemas de SD vs. el barbecho desnudo. Se realizó una búsqueda sistemática de la literatura que reporta los efectos de los CCI sobre los parámetros de abundancia, actividad y diversidad microbiana del suelo. Combinando 7 criterios de búsqueda se seleccionaron y analizaron 22 trabajos. El conjunto de resultados de esos trabajos muestra que la actividad enzimática del suelo se ve favorecida con la inclusión de CCI en la rotación, principalmente si estos se componen de leguminosas y mezclas de especies. Más de la mitad de esos trabajos reportan una mayor biomasa microbiana con CCI que con barbecho. Además, se advierte que los efectos de los CCI sobre los parámetros microbianos son independientes de la duración de los ensayos. Sin embargo, aún se necesitan más investigaciones básicas que permitan reducir la heterogeneidad entre estudios y comprender las complejas interacciones que ocurren entre los CCI y el microbioma del suelo.

Abstract The inclusion of winter cover crops (WCC) in no-till (NT) systems in replacement of bare fallow is a promising alternative to improve soil health and consequently, contribute to environmental sustainability of agricultural systems. This review provides a comprehensive evaluation of the effects of the use of WCC in rotation with summer cash crops under NT systems on the soil microbiome versus bare fallows. A systematic literature search was conducted to evaluate the impact of WCC on microbial parameters indicative of abundance, activity and diversity. Twenty-two papers were selected based on seven combined criteria. The results of this review show that enzyme activities in soil are enhanced with the inclusion of WCC in the rotation, particularly those that include legumes and mix of species. ln general, more than half of the analyzed papers report higher microbial biomass in soils with WCC than in bare fallow. Interestingly, the effects of WCC on microbial parameters are independent of the duration of the experiments. However, more basic research is necessary to reduce the heterogeneity of the studies and to better understand the complexity of the interactions between WCC and the soil microbiome.

[Effect of winter cover crops on the soil microbiome: a systematic literature review]. / Efecto de los cultivos de cobertura invernales sobre el microbioma del suelo: revisión sistemática de la literatura.

The inclusion of winter cover crops (WCC) in no-till (NT) systems in replacement of bare fallow is a promising alternative to improve soil health and consequently, contribute to environmental sustainability of agricultural systems. This review provides a comprehensive evaluation of the effects of the use of WCC in rotation with summer cash crops under NT systems on the soil microbiome versus bare fallows. A systematic literature search was conducted to evaluate the impact of WCC on microbial parameters indicative of abundance, activity and diversity. Twenty-two papers were selected based on seven combined criteria. The results of this review show that enzyme activities in soil are enhanced with the inclusion of WCC in the rotation, particularly those that include legumes and mix of species. In general, more than half of the analyzed papers report higher microbial biomass in soils with WCC than in bare fallow. Interestingly, the effects of WCC on microbial parameters are independent of the duration of the experiments. However, more basic research is necessary to reduce the heterogeneity of the studies and to better understand the complexity of the interactions between WCC and the soil microbiome.

Ammonia Oxidizing Prokaryotes Respond Differently to Fertilization and Termination Methods in Common Oat's Rhizosphere.

Cover crops (CC) have demonstrated beneficial effects on several soil properties yet questions remain regarding their effects on soil microbial communities. Among them, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) have a key role for N cycling in soil and their responses in the rhizosphere of terminated CC deserve further investigation. A greenhouse experiment was established to assess N fertilization (with or without N) and termination methods (glyphosate, mowing, and untreated control) of common oat (Avena sativa L.) as potential drivers of AOA and AOB responses in the rhizosphere. The abundance of amoA genes was determined by quantitative real-time PCR (qPCR), the community structure was assessed with Illumina amplicon sequencing of these genes, while the function was assessed from potential nitrification activity (PNA). While N fertilization had no influence on AOA, the termination method significantly increased amoA gene copies of AOA in mowed plants relative to glyphosate termination or the untreated control (1.76 and 1.49-fold change, respectively), and shifted AOA community structure (PERMANOVA, p<0.05). Ordination methods indicated a separation between AOA communities from control and glyphosate-terminated plants relative to mowed plants for both UniFrac and Aitchison distance. Converserly, N fertilization significantly increased AOB abundance in the rhizosphere of mowed and control plants, yet not in glyphosate-treated plants. Analyses of community structure showed that AOB changed only in response to N fertilization and not to the termination method. In line with these results, significantly higher PNA values were measured in all fertilized samples, regardless of the termination methods. Overall, the results of this study indicated that bacterial and archaeal nitrifiers have contrasting responses to fertlization and plant termination methods. While AOA were responsive to the termination method, AOB were more sensitive to N additions, although, the stimulative effect of N fertilization on amoA AOB abundance was dependent on the termination method.

Suppression treatment differentially influences the microbial community and the occurrence of broad host range plasmids in the rhizosphere of the model cover crop Avena sativa L.

Cover crop suppression with glyphosate-based herbicides (GBHs) represents a common agricultural practice. The objective of this study was to compare rhizospheric microbial communities of A. sativa plants treated with a GBH relative to the mechanical suppression (mowing) in order to assess their differences and the potential implications for soil processes. Samples were obtained at 4, 10, 17 and 26 days post-suppression. Soil catabolic profiling and DNA-based methods were applied. At 26 days, higher respiration responses and functional diversity indices (Shannon index and catabolic evenness) were observed under glyphosate suppression and a neat separation of catabolic profiles was detected in multivariate analysis. Sarcosine and Tween 20 showed the highest contribution to this separation. Metabarcoding revealed a non-significant effect of suppression method on either alpha-diversity metrics or beta-diversity. Conversely, differences were detected in the relative abundance of specific bacterial taxa. Mesorhizobium sequences were detected in higher relative abundance in glyphosate-treated plants at the end of the experiment while the opposite trend was observed for Gaiella. Quantitative PCR of amoA gene from ammonia-oxidizing archaea showed a lower abundance under GBH suppression again at 26 days, while ammonia-oxidizing bacteria remained lower at all sampling times. Broad host range plasmids IncP-1ß and IncP-1ε were exclusively detected in the rhizosphere of glyphosate-treated plants at 10 days and at 26 days, respectively. Overall, our study demonstrates differential effects of suppression methods on the abundance of specific bacterial taxa, on the physiology and mobile genetic elements of microbial communities while no differences were detected in taxonomic diversity.

Use of biogas digestates obtained by anaerobic digestion and co-digestion as fertilizers: Characterization, soil biological activity and growth dynamic of Lactuca sativa L.

Agro-industrial systems provide large quantities of organic wastes that could imply an important environmental risk. While manures can be easily treated by anaerobic digestion, horticultural fruit wastes generally cannot be processed alone and should be treated by co-digestion. To use organic wastes as fertilizers is fundamental to improve understanding of their impact on soil-plant systems. In this research, cattle manure, poultry litter, pig slurry and onion waste were collected. Animal manures were studied without treatment, treated by anaerobic digestion alone and in co-digestion with onion wastes. To study their effect on soil-plant systems, chemical and spectroscopic characterization of manures and their transformed products were combined with soil biological activity and growth dynamic of lettuce following wastes incorporation to the soil. Anaerobic digestion decreased the C/N ratio, whilst there was an increase in NH4+-N/N ratio and short-chain organic acids. The magnitude of these changes varied depending on the type of organic matter present in each material and the incorporation of onion wastes intensified them. However, the digestates presented similar structural characteristics to each other, independently of the material of origin. Digestate soil application produced a fast and short microbial stimulation (18-34 and 7-11 mg CO2 during the first 6 h, digestates vs. rest of treatments). The digestate dosage should be done according to the content of NH4+-N given that the vegetal growth is related to it. Soils amended with digestates showed less CO2 emission than soils amended with manures improving overall C balance.

Ecotoxicological assessment of soil microbial community tolerance to glyphosate.

Glyphosate is the most used herbicide worldwide. While contrasting results have been observed related with its impact on soil microbial communities, more studies are necessary to elucidate the potential effects of the herbicide. Differences in tolerance detected by Pollution Induced Community Tolerance (PICT) approach could reflect these effects. The objective of the present study was to assess the tolerance to glyphosate (the active ingredient and a commercial formulation) of contrasting soils with (H) and without (NH) history of exposure. The hypothesis of a higher tolerance in H soils due to a sustained selection pressure on community structure was tested through the PICT approach. Results indicated that tolerance to glyphosate is not consistent with previous history of exposure to the herbicide either for the active ingredient or for a commercial formulation. Soils of H and NH sites were also characterized in order to determine to what extent they differ in their functional diversity and structure of microbial communities. Denaturant Gradient Gel Electrophoresis (DGGE) and Quantitative Real Time PCR (Q-PCR) indicated high similarity of Eubacteria profiles as well as no significant differences in abundance, respectively, between H and NH sites. Community level physiological profiling (CLPP) indicated some differences in respiration of specific sources but functional diversity was very similar as reflected by catabolic evenness (E). These results support PICT assay, which ideally requires soils with differences in their exposure to the contaminant but minor differences in other characteristics. This is, to our knowledge, the first report of PICT approach with glyphosate examining tolerance at soil microbial community level.