Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment

Abstract

SummaryAnaerobic bacteria degrade lignocellulose in various anoxic and organically rich environments, often in a syntrophic process. Anaerobic enrichments of bacterial communities on a recalcitrant lignocellulose source were studied combining polymerase chain reaction–denaturing gradient gel electrophoresis, amplicon sequencing of the 16S rRNA gene and culturing. Three consortia were constructed using the microbiota of lake sediment as the starting inoculum and untreated switchgrass (Panicum virgatum) (acid or heat) or treated (with either acid or heat) as the sole source of carbonaceous compounds. Additionally, nitrate was used in order to limit sulfate reduction and methanogenesis. Bacterial growth took place, as evidenced from 3 to 4 log unit increases in the 16S rRNA gene copy numbers as well as direct cell counts through three transfers on cleaned and reused substrate placed in fresh mineral medium. After 2 days, Aeromonas bestiarum‐like organisms dominated the enrichments, irrespective of the substrate type. One month later, each substrate revealed major enrichments of organisms affiliated with different species of Clostridium. Moreover, only the heat‐treated substrate selected Dysgonomonas capnocytophagoides‐affiliated bacteria (Bacteroidetes). Towards the end of the experiment, members of the Proteobacteria (Aeromonas,Rhizobium and/or Serratia) became dominant in all three types of substrates. A total of 160 strains was isolated from the enrichments. Most of the strains tested (78%) were able to grow anaerobically on carboxymethyl cellulose and xylan. The final consortia yield attractive biological tools for the depolymerization of recalcitrant lignocellulosic materials and are proposed for the production of precursors of biofuels.

Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches

“…Here, we used an innovative enrichment strategy, with two stages, based on partially degraded plant biomass (once-used) as sole carbon source. A similar approach was recently used in an anaerobic enrichment from lake sediment using switchgrass (Korenblum et al 2016). Such a methodology is thought to enhance the prevalence of microbes acting on the most recalcitrant part of the lignocellulose (e.g.…”

Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia

“…The first one is the succession along the sequential transfers through the course of the enrichment process. Here, microbial communities are often tracked at the final growth stage, being compared against previous batches (on a weekly basis) [31]. The second type of succession occurs within the relatively 'stable' consortia, where microbial communities are evaluated within a unique culture batch (on a daily basis) (Figure 1B).…”

Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas

“…It is also worthwhile to compare broadly the phylum composition of lake sediment microbiota, which is typically dominated by Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Chiloroflexi (Krett & Palatinszky, 2009;Paul et al, 2016;Korenblum, Jiménez & Elsas, 2016). The phyla dominating the RMs in our subtropical lakeshore areas are similar to those occurring in terrestrial environments (Uroz et al, 2010;Mendes et al, 2011;Peiffer et al, 2013), despite the RMs we examined being dominated by Firmicutes, Proteobacteria, and Actinobacteira (Fig.…”