Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation

Abstract

There is now a great awareness of the high diversity of most environmental (“free-living”) and host-associated microbiomes, but exactly how diverse microbial communities form and maintain is still highly debated. A variety of theories have been put forward, but testing them has been problematic because most studies have been based on synthetic communities that fail to accurately mimic the natural composition (i.e., the species used are typically not found together in the same environment), the diversity (usually too low to be representative), or the environmental system itself (using designs with single carbon sources or solely mixed liquid cultures).

STrack: A Tool to Simply Track Bacterial Cells in Microscopy Time-Lapse Images

“…We focused on 4 bacterial species isolated from soil: Pseudomonas putida F1 ( 26 ), Pseudomonas veronii 1YdBTEX2 ( 27 ), Lysobacter sp., and Rahnella sp. (the 2 latter species coming from Causevic et al [ 28 ]). Cultures were recovered from −80°C stocks, and grown individually on nutrient agar, from which a single colony was transferred and grown in liquid media before being washed, diluted, and inoculated on the microscale-surfaces for imaging.…”

Fitness-Conditional Genes for Soil Adaptation in the Bioaugmentation Agent Pseudomonas veronii 1YdBTEX2

“…Both soils (silt and sand) were characterized for bacterial taxonomic diversity using amplicon analysis of the V3-V4 region of the 16S rRNA gene on purified DNA, as described ( 84 ). Raw reads are available from a single downloadable link [ 57 ].…”

Environmental microbiome engineering for the mitigation of climate change

“…Generational stability is achieved by incubating communities for long enough that after each passage, they converge to the same taxonomic and functional composition from one generation to the next, which tightens the relationship between community structure and function (Sánchez et al, 2021). Generational stability can take between 12 and 21 days, depending on the environment (Bittleston et al, 2020; Goldford et al, 2018; Zegeye et al, 2019), and longer incubation periods (2 and 6 months) generate more community diversity than short incubation periods (1 week) in soil (Čaušević et al, 2022). Perturbing these stable communities with the delivery of a diverse pool of species or nutrients regenerates trait variation and increases the chances of finding a community with even higher trait expression on the subsequent selection cycle.…”

“…By contrast, culturing inocula in liquid carriers is fast, scalable, has a longer shelf life, and can be easier to deliver to the environment than solid carriers (Allouzi et al, 2022). However, liquid can restructure inocula (Čaušević et al, 2022; Howard et al, 2017; Zegeye et al, 2019) and reduce the capacity for establishment into a solid, spatially structured target environment like soil. In one study, soil communities were enriched with chitin and then cultured with its monomer N‐acetylglucosamine in sterile soil and liquid minimal media at serial dilutions (Zegeye et al, 2019).…”

“…Overall, liquid communities exhibited lower diversity; however, they displayed less volatile dynamics than soil communities over time, which may prove beneficial in maintaining inocula communities at industrial scales (Howard et al, 2017; Zegeye et al, 2019). Many of the same bacterial phyla were shared between treatments, especially at lower dilutions (Zegeye et al, 2019) or with longer incubation times (Čaušević et al, 2022). While scaling the production of inocula in liquid will impose selective pressures, these results showed that liquid cultures stabilize more quickly than those grown in a solid substrate and that nutrient supplementation can preserve the deeper lineage structure of communities (Zegeye et al, 2019).…”