Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility

Abstract

Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I (“Slash-and-burn deforestation”) the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II (“Management practices for sugarcane”) disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-015-0530-3) contains supplementary material, which is available to authorized users.

RETRACTED: Effect of Plant Extracts and Metam Sodium on the Soilborne Fungal Pathogens, Meloidogyne spp., and Soil Microbial Community

“…Nevertheless, other researchers have come to different conclusions based on similar results. Navarrete et al [56], for instance, correlated an increase in Verrucomicrobia with low soil fertility.…”

Agronomic and environmental implications of sugarcane straw removal: a major review

“…All these studies have shown that individuals within the phylum Verrucomicrobia often benefit and become more abundant in areas that lack a straw covering. Members of this phylum have been described as highly selective for areas of low soil fertility and poor soil quality (Navarrete et al ., ). It is therefore likely that this taxonomic group might be effectively used to monitor the biological depletion of soil quality in sugarcane fields.…”

“…() observed that straw removal modified the fungal communities present in soil, but did not affect bacterial communities. However, other studies have shown that microbial communities can be shaped by straw management as well as through the addition of organic or mineral fertilizers (Rachid et al ., ; Navarrete et al ., ; Pitombo et al ., ). All these studies have shown that individuals within the phylum Verrucomicrobia often benefit and become more abundant in areas that lack a straw covering.…”

The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment

“…Indeed, while a recent study suggested that members of this phylum favour higher moisture soils (Maestre et al, 2015), another study noted that their abundance increased following droughts and heat waves (Acosta-Martinez et al, 2014) and Buckley et al (2001) suggest that they are negatively associated with moisture. As with the Acidobacteria, the ecology of soil Verrucomicrobia is poorly understood; however, evidence for their abundance in soil is increasing, in particular, in grassland biomes (Buckley & Schmidt, 2001;Bergmann et al, 2011;Fierer et al, 2013;Carbonetto et al, 2014;Navarrete et al, 2015). This study provides further support for the Verrucomicrobia dominance of soil microbial communities and suggests that members of this phylum and, more specifically, the class Spartobacteria show variability in their response to moisture, even within a single habitat, suggesting that they may have a diverse functional role in soil.…”