Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments

Abstract

Alkanes are major constituents of plant-derived waxy materials. In this study, we investigated the abundance, community structure and activity of bacteria harbouring the alkane monooxygenase gene alkB, which catalyses a major step in the pathway of aerobic alkane degradation in the litter layer, the litter-soil interface and in bulk soil at three time points during the degradation of maize and pea plant litter (2, 8 and 30 weeks) to improve our understanding about drivers for microbial performance in different soil compartments. Soil cores of different soil textures (sandy and silty) were taken from an agricultural field and incubated at constant laboratory conditions. The abundance of alkB genes and transcripts (by qPCR) as well as the community structure (by terminal restriction fragment polymorphism fingerprinting) were measured in combination with the concentrations and composition of alkanes. The results obtained indicate a clear response pattern of all investigated biotic and abiotic parameters depending on the applied litter material, the type of soil used, the time point of sampling and the soil compartment studied. As expected the distribution of alkanes of different chain length formed a steep gradient from the litter layer to the bulk soil. Mainly in the two upper soil compartments community structure and abundance patterns of alkB were driven by the applied litter type and its degradation. Surprisingly, the differences between the compartments in one soil were more pronounced than the differences between similar compartments in the two soils studied. This indicates the necessity for analysing processes in different soil compartments to improve our mechanistic understanding of the dynamics of distinct functional groups of microbes.

Plant <i>n</i>-alkane production from litterfall altered the diversity and community structure of alkane degrading bacteria in litter layer in lowland subtropical rainforest in Taiwan

“…They could, however, proliferate in the habitats with the appropriate substrate supplements. This finding is consistent with the results from a previous study using a laboratory-controlled system and an agricultural research farm (Schulz et al, 2012;Giebler et al, 2013).…”

“…The litter-leaf, the main component of litterfall, similarly provides the major source of plantderived alkanes. The significant effects of litterfall derived alkanes on the bacterial alkane degradation potential have also been observed (Giebler et al, 2013 andSchulz et al, 2012). As the litterfall in the habitats of the Nanjenshan Reserve was different, investigation into the effects of litterfall on various habitats and microbial communities in these habitats is possible.…”

“…The dynamic changes in alkB-degrading bacteria populations were demonstrated to be driven by numerous factors, such as the original source of the alkane and soil type. Although knowledge of the regulatory mechanisms regarding environmental plant litter on soil bacterial levels and of the dynamics of alkane-degrading bacteria in natural habitats has been beneficial and important in many aspects, studies on their dynamic changes are currently lacking and should be conducted (Schulz et al, 2012).…”

Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance

“…Other recent studies have also shown that disturbance from shifts in climate (Yergeau et al, 2012a), differences in local environmental factors (Pommier et al, 2012), and distance from the litter layer (Schulz et al, 2012) have a greater effect than geography in determining microbial community composition. Metagenomic studies have shown that discrete taxonomic units exist within bacteria (Caro-Quintero and Konstantinidis, 2012), and our data demonstrate that taxonomic affiliation does affect which organisms will dominate in particular contaminated soils.…”

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

“…We took soil samples after maturation phases of either 3 (T3) or 12 months (T12), in which we analysed the abundance (quantitative PCR, qPCR, Supplementary Material S1.2) and community structure (terminal restriction fragment length polymorphism analysis, T-RFLP, Supplementary Material S1.3) of alkane-degrading microbes, as well as response patterns towards the addition of plant litter from winter wheat after 2 weeks of incubation subsequent to maturation. Schulz et al (2012) described the alkane monooxygenase gene (alkB) as a sensitive marker for the molecular analysis of alkane-degrading bacteria responding to subtle changes in substrate availability that is, fresh plant material, which in general contains large amounts of easily available alkanes in form of waxes. The litter was added on top of the microcosms to create a vertical substrate gradient.…”