Microbiome dynamics of disease suppresive soils

Abstract

The genus Lysobacter includes several species that produce a range of extracellular enzymes and other metabolites with activity against bacteria, fungi, oomycetes and nematodes. Lysobacter species were found to be more abundant in soil suppressive against the fungal root pathogen Rhizoctonia solani, but their actual role in disease suppression is still unclear. Here, the antifungal and plant growth-promoting activities of 18Lysobacter strains, including 11 strains from Rhizoctonia suppressive soils, were studied both in vitro and in vivo. Based on 16S rRNA sequencing, the Lysobacter strains from the Rhizoctonia suppressive soil belonged to the four species L. antibioticus, L. capsici, L. enzymogenes and L. gummosus. Most strains showed strong in vitro activity against R. solani and several other pathogens, including Pythium ultimum, Aspergillus niger, Fusarium oxysporum and Xanthomonas campestris. When the Lysobacter strains were introduced into soil, however, no significant and consistent suppression of R. solani damping-off disease of sugar beet and cauliflower was observed. Subsequent bioassays further revealed that none of the Lysobacter strains was able to promote growth of sugar beet, cauliflower, onion and Arabidopsis thaliana, either directly or via volatile compounds. The lack of in vivo activity is most likely attributed to poor colonization of the rhizosphere by the introduced Lysobacter strains. In conclusion, our results demonstrated that Lysobacter species have strong antagonistic activities against a range of pathogens, making them an important source for putative new enzymes and antimicrobial compounds. However, their potential role in R. solani disease suppressive soil could not be confirmed. In-depth omics'-based analyses will be needed to shed more light on the potential contribution of Lysobacter species to the collective activities of microbial consortia in disease suppressive soils.

Rhizoctonia solanidisease suppression: addition of keratin-rich soil amendment leads to functional shifts in soil microbial communities

“…What does the succession look like or are some community members able to perform the complete degradation pathway alone or only as a group are questions not to be answered with the data available. Comparing more enriched taxa in amendment-induced R. solani suppressive soils from this study and Andreo-Jimenez et al (Andreo-Jimenez et al, 2021) with those from successive monocropping strategies resulted in comparable microbiome patterns including a higher abundance of Pseudomonadaceae, Sphingomonadaceae, Burkholderiaceae, Xanthomonadales, Oxalobacteraceae, Caulobacteraceae, Sphingobacteriaceae, Chitinophagaceae and Flavobacteriaceae in disease suppressive soils (Chapelle et al, 2016;Cordovez et al, 2015;Expósito, 2017;Mendes et al, 2011;Yin et al, 2021). It seems that selected organic amendments can stimulate the same groups that are associated with disease suppression without the addition of an amendment.…”

“…Take-all decline is defined as the spontaneous reduction in the incidence and severity of the disease and increase in yield occurring with continuous monoculture of the host crop following a severe attack of the disease (Schlatter et al, 2017). Also, for R. solani-induced diseases a decline has been reported in both field and pot experiments for several crops, i.e., wheat (Lucas et al, 1993;Mazzola & Gu, 2002;Roget, 1995;Wiseman et al, 1996), sugar beet (Expósito, 2017;Hyakumachi et al, 1990;Sayama et al, 2001), radish (Chern & Ko, 1989;Chet & Baker, 1980;Henis et al, 1978), potato (Jager & Velvis, 1995;Velvis et al, 1989) and cauliflower (Davik & Sundheim, 1984;Postma et al, 2010). The second approach to stimulate disease suppression requires the addition of organic amendments into soils.…”

“…Disregarding the approach to induce Rhizoctonia suppressiveness in soils, several organisms or combinations thereof were commonly found to correlate with lower disease incidence in different crops and soils. These include members of the bacterial families Oxalobacteriaceae, Comamonadaceae and Burkholderiaceae, Pseudomonadaceae as well as members of the orders Hyphomicrobiales and Sphingobacteriales (notably Flavobacterium, Chryseobacteria and Chitinophaga) and the fungal family Mortierellaceae (Andreo-Jimenez et al, 2021;Bonanomi et al, 2010;Carrión et al, 2018;Carrión et al, 2019;Chapelle et al, 2016;Expósito, 2017;Gómez Expósito et al, 2017;Yin et al, 2021). A universal pattern of the responsible microorganisms and especially the underlying mechanisms for Rhizoctonia suppressive soils is still lacking, although several potential mechanisms of disease suppression have been proposed.…”

Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings

“…were previously found within sugar beet plants challenged by Rhizoctonia solani and were associated with a higher expression of chitinases (Carrión et al ., 2019 ). Spingobacteriaceae were also found in disease suppressive soils and showed antagonistic activity against plant‐pathogenic fungi, when triggered by interaction with other members of the bacterial community (de Boer et al ., 2007 ; Gómez Expósito, 2017 ). Although Rhizobiales are mostly known as N‐fixing mutualists of legumes, they can also establish mutualistic interactions with non‐legume plants and contribute to plant growth stimulation and priming of the plant immune system (Garrido‐Oter et al ., 2018 ).…”

Investigating the Energy-Water Usage Efficiency of the Reuse of Treated Municipal Wastewater for Artificial Groundwater Recharge

“…Each different geographic region is characterized by a different portfolio of energy generation technologies that is responsible for the production of the electricity being locally consumed. , This portfolio is typically referred to as the local grid mix. It has been observed by others that, depending upon the composition of generation technologies comprising this grid mix, the consumption of electricity within a region can be associated with non trivial withdrawals and or consumption of freshwater due to such processes as the cooling of thermoelectric coal and natural gas fired power plants or the evaporative losses from reservoirs associated with the operation of hydroelectric dams. − …”