Title: Bacterial diversity dynamics in microbial consortia selected for lignin utilization

Abstract

Lignin is nature’s largest source of phenolic compounds. Its recalcitrance to enzymatic conversion is still a limiting step to increase the value of lignin. Although bacteria are able to degrade lignin in nature, most studies have focused on lignin degradation by fungi. To understand which bacteria are able to use lignin as the sole carbon source, natural selection over time was used to obtain enriched microbial consortia over a 12-week period. The source of microorganisms to establish these microbial consortia were commercial and backyard compost soils. Cultivation occurred at two different temperatures, 30°C and 37°C, in defined culture media containing either Kraft lignin or alkaline-extracted lignin as carbon source. iTag DNA sequencing of bacterial 16S rDNA gene was performed for each of the consortia at six timepoints (passages). The initial bacterial richness and diversity of backyard compost soil consortia was greater than that of commercial soil consortia, and both parameters decreased after the enrichment protocol, corroborating that selection was occurring. Bacterial consortia composition tended to stabilize from the fourth passage on. After the enrichment protocol, Firmicutes phylum bacteria were predominant when lignin extracted by alkaline method was used as a carbon source, whereas Proteobacteria were predominant when Kraft lignin wasmore » used. Bray-Curtis dissimilarity calculations at genus level, visualized using NMDS plots, showed that the type of lignin used as a carbon source contributed more to differentiate the bacterial consortia than the variable temperature. The main known bacterial genera selected to use lignin as a carbon source were Altererythrobacter, Aminobacter, Bacillus, Burkholderia, Lysinibacillus, Microvirga, Mycobacterium, Ochrobactrum, Paenibacillus, Pseudomonas, Pseudoxanthomonas, Rhizobiales and Sphingobium. These selected bacterial genera can be of particular interest for studying lignin degradation and utilization, as well as for lignin-related biotechnology applications.« less

Authors:

Mendes, Isis Viana ^[1]; Garcia, Mariana Botelho ^[2]; Bitencourt, Ana Carolina Araújo ^[1]; Santana, Renata Henrique ^[3]; Lins, Philippe de Castro ^[1]; Silveira, Rafaella ^[4]; Simmons, Blake A. ^[5]; Gladden, John M. ^[6]; Kruger, Ricardo Henrique ^[4]; Quirino, Betania Ferraz  ^[7]

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+ Show Author Affiliations

1. Parque Estação Biológica (PqEB), Brasilia (Brazil); Univ. of Brasilia (Brazil)
2. Parque Estação Biológica (PqEB), Brasilia (Brazil); Catholic Univ. of Brasilia (Brazil)
3. Federal Institute of Brasilia (Brazil)
4. Univ. of Brasilia (Brazil)
5. Joint BioEnergy Institute (JBEI), Emeryville, CA (United States)
6. Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
7. Parque Estação Biológica (PqEB), Brasilia (Brazil); Univ. of Brasilia (Brazil); Catholic Univ. of Brasilia (Brazil)

Publication Date:

Mon Sep 13 00:00:00 EDT 2021

Research Org.:

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:

1826058

Grant/Contract Number:  

AC02-05CH11231

Resource Type:

Accepted Manuscript

Journal Name:

PLoS ONE

Additional Journal Information:

Journal Volume: 16; Journal Issue: 9; Journal ID: ISSN 1932-6203

Publisher:

Public Library of Science

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; Lignin; Consortia; Bacteria; Bacterial taxonomy; Burkholderia; Agricultural soil science; Graphs; Microbial taxonomy