Fungal community shifts in soils with varied cover crop treatments and edaphic properties

Algae communication, conspecific and interspecific: the concepts of phycosphere and algal-bacteria consortia in a photobioreactor (PBR)

Microalgae in the wild often form consortia with other species promoting their own health and resource foraging opportunities. The recent application of microalgae cultivation and deployment in commercial photobioreactors (PBR) so far has focussed on single species of algae, resulting in multi-species consortia being largely unexplored. Reviewing the current status of PBR ecological habitat, this article argues in favor of further investigation into algal communication with conspecifics and interspecifics, including other strains of microalgae and bacteria. These mutualistic species form the 'phycosphere': the microenvironment surrounding microalgal cells, potentiating the production of certain metabolites through biochemical interaction with cohabitating microorganisms. A better understanding of the phycosphere could lead to novel PBR configurations, capable of incorporating algal-microbial consortia, potentially proving more effective than single-species algal systems.

Mycosorb A+® como adsorbente de micotoxinas en la dieta sobre la salud y la producción en cuyes

Los alimentos destinados a los animales están contaminados por hongos filamentosos que producen micotoxinas. El estudio tuvo como objetivo evaluar el efecto de Mycosorb A+® como adsorbente de micotoxinas en la dieta sobre la salud, producción y beneficio económico de cuyes en crianza comercial. Se utilizaron 80 cuyes en crecimiento de la raza Perú, entre machos y hembras, con un peso de 435,5 ± 35,5 gramos (g), distribuidos al azar en dos grupos de alimentación: dieta con Mycosorb A+® (experimental) y dieta sin Mycosorb A+® (control), realizado en el distrito de Ilabaya-Tacna, Perú, a 1.425 metros de altitud, durante 57 días. La dieta se elaboró con heno molido de alfalfa, maíz amarillo, afrecho de trigo, torta de soya, harina integral de soya y fuentes de minerales y vitaminas, ofrecida para consumo ad libitum, más 12,5 g·día-1 de alfalfa fresca (H° 78 %) por cuy. Los resultados indican que todas las variables evaluadas, excepto el consumo de materia seca, fueron significativas (P<0,05): morbilidad 2,5 vs. 35,0 %; consumo de materia seca, 59,8 ± 2,1 vs. 58,0 ± 2,4 g·día-1; ganancia de peso vivo, 9,7 ± 1,4 vs. 7,8 ± 0,9 g·día-1; conversión alimenticia, 6,3 ± 0,9 vs. 7,5 ± 0,6; y relación beneficio-costo, 1,52 vs. 1,35, respectivamente. Se concluye que la inclusión de Mycosorb A+® como adsorbente de micotoxinas en la dieta tiene efecto positivo en la salud, producción y beneficio económico en la crianza comercial de cuyes.

Leguminous cover crops and soya increased soil fungal diversity and suppressed pathotrophs caused by continuous cereal cropping

The enrichment of soil-borne fungal pathogens and a high input of mineral fertilizer in the continuous cropping of cereal crops have raised a concern about soil health deterioration. Conversion of continuous cereal cropping to a legume-involved system alters the soil fungal community. However, when a leguminous cover crop is grown with a succeeding legume grain crop such as soya (Glycine max L. Merril), the effects on the soil fungal community when two legumes are involved in the crop system remain unclear. Thus, the effects of the cover crop on the soil fungal community under a succession of soya and a succession of maize (Zea mays L.) were clarified: a continuous wheat (Triticum aestivum L.)-maize cropping system was converted to new rotation systems with three cover crop treatments: leguminous vetch (Vicia sativa L.), a mixture of vetch and rye (Secale cereale L.), and fallow, succeeded by soya or maize in this study. The soil fungal community at the harvest of soya and maize were determined using high-throughput sequencing of ITS2 amplicons. Compared to a wheat-maize rotation system, all of the new rotation systems that involved leguminous crops or fallow increased the soil fungal diversity and suppressed pathotrophs by reducing the soil NH4 +, NO3 -, available K, and available P concentrations. Different cover crops changed the fungal community composition, but their effect was overwhelmed by the strong effect of succeeding soya, which induced minor shifts among the cover crop treatments under soya than maize. The Vetch-Soya system exhibited the highest fungal diversity, which have been due to an increase of symbiotrophs. Replacing wheat with mixed vetch and rye most greatly suppressed the pathotrophs, and this suppression effect was stronger when succeeded by maize than by soya. These results showed the short-term benefits of legume-legume succession and legume-cereal mixed cover crops for increasing fungal diversity and suppressing pathotrophs. Further study is needed to examine the long-term effects of Vetch-Soya on the accumulation of legume-associated pathogens.

Endophytic Metarhizium robertsii suppresses the phytopathogen, Cochliobolus heterostrophus and modulates maize defenses

Fungi in the genus Metarhizium (Hypocreales: Clavicipitaceae) are insect-pathogens and endophytes that can benefit their host plant through growth promotion and protection against stresses. Cochliobolus heterostrophus (Drechsler) Drechsler (Pleosporales: Pleosporaceae) is an economically-significant phytopathogenic fungus that causes Southern Corn Leaf Blight (SCLB) in maize. We conducted greenhouse and lab-based experiments to determine the effects of endophytic M. robertsii J.F. Bisch., Rehner & Humber on growth and defense in maize (Zea mays L.) infected with C. heterostrophus. We inoculated maize seeds with spores of M. robertsii and, at the 3 to 4-leaf stage, the youngest true leaf of M. robertsii-treated and untreated control plants with spores of C. heterostrophus. After 96 h, we measured maize height, above-ground biomass, endophytic colonization by M. robertsii, severity of SCLB, and expression of plant defense genes and phytohormone content. We recovered M. robertsii from 74% of plants grown from treated seed. The severity of SCLB in M. robertsii-treated maize plants was lower than in plants inoculated only with C. heterostrophus. M. robertsii-treated maize inoculated or not inoculated with C. heterostrophus showed greater height and above-ground biomass compared with untreated control plants. Height and above-ground biomass of maize co-inoculated with M. robertsii and C. heterostrophus were not different from M. robertsii-treated maize. M. robertsii modulated the expression of defense genes and the phytohormone content in maize inoculated with C. heterostrophus compared with plants not inoculated with C. heterostrophus and control plants. These results suggest that endophytic M. robertsii can promote maize growth and reduce development of SCLB, possibly by induced systemic resistance mediated by modulation of phytohormones and expression of defense and growth-related genes in maize.

Cover crop-driven shifts in soil microbial communities could modulate early tomato biomass via plant-soil feedbacks

Sustainable agricultural practices such as cover crops (CCs) and residue retention are increasingly applied to counteract detrimental consequences on natural resources. Since agriculture affects soil properties partly via microbial communities, it is critical to understand how these respond to different management practices. Our study analyzed five CC treatments (oat, rye, radish, rye-radish mixture and no-CC) and two crop residue managements (retention/R+ or removal/R-) in an 8-year diverse horticultural crop rotation trial from ON, Canada. CC effects were small but stronger than those of residue management. Radish-based CCs tended to be the most beneficial for both microbial abundance and richness, yet detrimental for fungal evenness. CC species, in particular radish, also shaped fungal and, to a lesser extent, prokaryotic community composition. Crop residues modulated CC effects on bacterial abundance and fungal evenness (i.e., more sensitive in R- than R+), as well as microbial taxa. Several microbial structure features (e.g., composition, taxa within Actinobacteria, Firmicutes and Ascomycota), some affected by CCs, were correlated with early biomass production of the following tomato crop. Our study suggests that, whereas mid-term CC effects were small, they need to be better understood as they could be influencing cash crop productivity via plant-soil feedbacks.

The biological sink of atmospheric H2 is more sensitive to spatial variation of microbial diversity than N2O and CO2 emissions in a winter cover crop field trial

The integration of winter cover crop (WCC) in culture rotations promotes multiple ecosystem services, but concomitant microbial diversity and functioning responses in soil have received less attention. A field trial was established to test the hypothesis that enhanced crop diversity with the integration of WCC in a conventional maize-soy rotation promotes microbial diversity and the biological sink of H₂ in soil, while reducing N₂O emissions to the atmosphere. Vicia villosa (hairy vetch), Avena sativa (oat), and Raphanus sativus (Daikon radish) were cultivated alone or in combinations and flux measurements were performed throughout two subsequent growing seasons. Soil acted as a net sink for H₂ and as a net source for CO₂ and N₂O. CO₂ flux was the most sensitive to WCC whereas a significant spatial variation was observed for H₂ flux with soil uptake rates observed in the most productive area two-fold greater than the baseline level. Sequencing and quantification of taxonomic and functional genes were integrated to explain variation in trace gas fluxes with compositional changes in soil microbial communities. Fungal communities were the most sensitive to WCC, but neither community abundance nor beta diversity were found to be indicative of fluxes. The alpha diversity of taxonomic and functional genes, expressed as the number of effective species, was integrated into composite variables extracted from multivariate analyses. Only the composite variable computed with the inverse Simpson's index displayed a reproducible pattern throughout both growing seasons, with functional genes and bacterial 16S rRNA gene defining the two most contrasting gradients. The composite variable was decoupled from WCC treatment and explained 19-20% spatial variation of H₂ fluxes. The coupling of composite alpha diversity metrics derived from multiple genes with soil processes warrants further investigations to implement novel indicators of soil health in response to changing management practices at the local scale.

Links Among Crop Diversification, Microbial Diversity, and Soil Organic Carbon: Mini Review and Case Studies

Interactions between species above- and belowground are among the top factors that govern ecosystem functioning including soil organic carbon (SOC) storage. In agroecosystems, understanding how crop diversification affects soil biodiversity and SOC storage at the local scale remains a key challenge for addressing soil degradation and biodiversity loss that plague these systems. Yet, outcomes of crop diversification for soil microbial diversity and SOC storage, which are key indicators of soil health, are not always positive but rather they are highly idiosyncratic to agroecosystems. Using five case studies, we highlight the importance of selecting ideal crop functional types (as opposed to focusing on plant diversity) when considering diversification options for maximizing SOC accumulation. Some crop functional types and crop diversification approaches are better suited for enhancing SOC at particular sites, though SOC responses to crop diversification can vary annually and with duration of crop cover. We also highlight how SOC responses to crop diversification are more easily interpretable through changes in microbial community composition (as opposed to microbial diversity). We then develop suggestions for future crop diversification experiment standardization including (1) optimizing sampling effort and sequencing depth for soil microbial communities and (2) understanding the mechanisms guiding responses of SOC functional pools with varying stability to crop diversification. We expect that these suggestions will move knowledge forward about biodiversity and ecosystem functioning in agroecosystems, and ultimately be of use to producers for optimizing soil health in their croplands.

Soil Mycobiome Is Shaped by Vegetation and Microhabitats: A Regional-Scale Study in Southeastern Brazil

Soil is the principal habitat and reservoir of fungi that act on ecological processes vital for life on Earth. Understanding soil fungal community structures and the patterns of species distribution is crucial, considering climatic change and the increasing anthropic impacts affecting nature. We evaluated the soil fungal diversity in southeastern Brazil, in a transitional region that harbors patches of distinct biomes and ecoregions. The samples originated from eight habitats, namely: semi-deciduous forest, Brazilian savanna, pasture, coffee and sugarcane plantation, abandoned buildings, owls' and armadillos' burrows. Forty-four soil samples collected in two periods were evaluated by metagenomic approaches, focusing on the high-throughput DNA sequencing of the ITS2 rDNA region in the Illumina platform. Normalized difference vegetation index (NDVI) was used for vegetation cover analysis. NDVI values showed a linear relationship with both diversity and richness, reinforcing the importance of a healthy vegetation for the establishment of a diverse and complex fungal community. The owls' burrows presented a peculiar fungal composition, including high rates of Onygenales, commonly associated with keratinous animal wastes, and Trichosporonales, a group of basidiomycetous yeasts. Levels of organic matter and copper influenced all guild communities analyzed, supporting them as important drivers in shaping the fungal communities' structures.

Plant Microbiota Beyond Farming Practices: A Review

Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.

Western Corn Rootworm, Plant and Microbe Interactions: A Review and Prospects for New Management Tools

The western corn rootworm, Diabrotica virgifera virgifera LeConte, is resistant to four separate classes of traditional insecticides, all Bacillius thuringiensis (Bt) toxins currently registered for commercial use, crop rotation, innate plant resistance factors, and even double-stranded RNA (dsRNA) targeting essential genes via environmental RNA interference (RNAi), which has not been sold commercially to date. Clearly, additional tools are needed as management options. In this review, we discuss the state-of-the-art knowledge about biotic factors influencing herbivore success, including host location and recognition, plant defensive traits, plant-microbe interactions, and herbivore-pathogens/predator interactions. We then translate this knowledge into potential new management tools and improved biological control.

Microbial Community Dynamics of Soybean (Glycine max) Is Affected by Cropping Sequence

The microbial composition of the rhizosphere soil could be an important determinant of crop yield, pathogen resistance, and other beneficial attributes in plants. However, little is known about the impact of cropping sequences on microbial community dynamics, especially in economically important species like soybean. Using 2-year crop sequences of corn-soybean, canola-soybean, and soybean-soybean, we investigated how crops from the previous growing season influenced the structure of the microbiome in both the bulk soil and soybean rhizosphere. A combination of marker-based Illumina sequencing and bioinformatics analyses was used to show that bacterial species richness and evenness in the soybean rhizosphere soil were similar following canola and soybean compared to a previous corn sequence. However, fungal species richness and evenness remained unaffected by crop sequence. In addition, bacterial and fungal species diversity in both the bulk and soybean rhizosphere soil were not influenced by crop sequence. Lastly, the corn-soybean sequence significantly differed in the relative abundance of certain bacterial and fungal classes in both the soybean rhizosphere and bulk soil. While canola-soybean and a continuous soybean sequence did not, suggesting that a preceding corn sequence may reduce the occurrence of overall bacterial and fungal community members. For the present study, crop sequence impacts bacterial diversity and richness in both the bulk soil and soybean rhizosphere soil whereas fungal diversity and richness are resilient to crop sequence practices. Together, these findings could help drive decision making for annual crop and soil management practices.