Long-Term Enrichment of Stress-Tolerant Cellulolytic Soil Populations following Timber Harvesting Evidenced by Multi-Omic Stable Isotope Probing

Abstract

Soil management is vital for maintaining the productivity of commercial forests, yet the long-term impact of timber harvesting on soil microbial communities remains largely a matter of conjecture. Decomposition of plant biomass, comprised mainly of lignocellulose, has a broad impact on nutrient cycling, microbial activity and physicochemical characteristics of soil. At “Long-term Soil Productivity Study” sites in California dominated by Ponderosa pine, we tested whether clear-cut timber harvesting, accompanied by varying degrees of organic matter (OM) removal, affected the activity and structure of the cellulose-degrading microbial populations 16 years after harvesting. Using a variety of experimental approaches, including stable isotope probing with 13C-labeled cellulose in soil microcosms, we demonstrated that harvesting led to a decrease in net respiration and cellulolytic activity. The decrease in cellulolytic activity was associated with an increased relative abundance of thermophilic, cellulolytic fungi (Chaetomiaceae), coupled with a decreased relative abundance of cellulolytic bacteria, particularly members of Opitutaceae, Caulobacter, and Streptomycetaceae. In general, harvesting led to an increase in stress-tolerant taxa (i.e., also non-cellulolytic taxa), though our results indicated that OM retention mitigated population shifts via buffering against abiotic changes. Stable-isotope probing improved shotgun metagenome assembly by 20-fold and enabled the recovery of 10 metagenome-assembled genomes of cellulolytic bacteria and fungi. Our study demonstrates the putative cellulolytic activity of a number of uncultured taxa and highlights the mineral soil layer as a reservoir of uncharacterized diversity of cellulose-degraders. It also and contributes to a growing body of research showing persistent changes in microbial community structure in the decades following forest harvesting.

Following the terrestrial tracks of Caulobacter - redefining the ecology of a reputed aquatic oligotroph

“…The number of culturable Caulobacter significantly decreased when soil was dried and increased when soil was agitated in water prior to culturing [5,36]. Similarly, the deleterious effect of prolonged exposure to dry conditions was evident in the decline of soil Caulobacter populations in the decades following timber harvesting [37] and in a soil warming experiment [38]. The reduction in Caulobacter populations in drier soil is likely due to attrition from the inability of irreversibly bound cells to disperse and colonize new resources.…”

Competitive exclusion and metabolic dependency among microorganisms structure the cellulose economy of agricultural soil

“…Chaetomium were also found to be successionists in clear-cut forest soils [40]. The most abundant endoglucanase in our metaproteome, a GH9 from Cellvibrio, was the major cellulase found in worm castings derived from an agricultural soil (ACY24809) [41].…”

Bacterial and fungal contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

“…Many of the novel cellulolytic groups we identified belong to cultivation-resistant phyla, Planctomycetes, Verrucomicrobia, Chloroflexi and Armatimonadetes (formerly 0P10), which commonly predominate soil communities (Youssef et al , 2009; Bergmann et al , 2011). Each of these phyla possesses at least one isolate capable of degrading cellulose (Sangwan et al , 2004; Lladó et al , 2015; Dedysh et al , 2013; Lee et al , 2014) and have been designated cellulolytic in other SIP-cellulose experiments Eichorst and Kuske, 2012; Verastegui et al , 2014; Pepe-Ranney and Campbell et al , 2016; Wilhelm a et al , 2017). Notably, all contigs that contained clusters of ten or more CAZymes (27 contigs), from 13 C-cellulose metagenomes, were classified to taxa from the aforementioned groups and contained both CBMs (26/27) and endoglucanases (20/27).…”

“…The extent to which catabolic traits are conserved within specific taxa versus communities will influence models of microbial decomposition. In the simplest case, the abundance of highly adapted, multi-substrate degrading taxa may predict rates of decomposition, which is supported by a small number of studies (Strickland et al , 2009; Wilhelm a et al , 2017). However, forces of genomic streamlining in bacteria lead to functional diversification among closely related species, particularly in extra-cellular processes that produce common goods (Morris et al , 2012), evident in the species-level conservation of bacterial endoglucanases (Berlemont and Martiny, 2013).…”

“…The identity of degraders and their genomic content were assessed using amplicon and shotgun sequencing of DNA enriched in 13 C from labeled substrates.Lignocellulolytic activity was quantified according to the amount of 13 C assimilated into total DNA and phospholipid fatty acids (PLFA). The in situ abundances of lignocellulolytic populations were determined on the basis of previously reported pyrotag libraries from the same field samples (Wilhelm et al , 2017 b , Wilhelm et al , 2017 c ). This is currently the most comprehensive cultivation-independent study of lignocellulolytic populations in forest soils and yields new insights to the taxa responsible and the importance of certain catabolic gene families.…”