Non‐random processes determine the colonization of groundwater sediments by microbial communities in a pristine porous aquifer

Abstract

Summary Sediments accommodate the dominating share of groundwater microbiomes, however the processes that govern the assembly and succession of sediment‐attached microbial communities in groundwater aquifers are not well understood. To elucidate these processes, we followed the microbial colonization of sterile sediments in in situ microcosms that were exposed to groundwater for almost 1 year at two distant but hydrologically connected sites of a pristine, shallow, porous aquifer. Our results revealed intriguing similarities between the community succession on the newly‐colonized sediments and succession patterns previously observed for biofilms in other more dynamic aquatic environments, indicating that the assembly of microbial communities on surfaces may be governed by similar underlying mechanisms across a wide range of different habitats. Null model simulations on spatiotemporally resolved 16S rRNA amplicon sequencing data further indicated selection of specific OTUs rather than random colonization as the main driver of community assembly. A small fraction of persistent OTUs that had established on the sediments during the first 115 days dominated the final communities (68%–85%), suggesting a key role of these early‐colonizing organisms, in particular specific genera within the Comamonadaceae and Oxalobacteraceae, for community assembly and succession during the colonization of the sediments. Overall, our study suggests that differences between planktonic and sediment‐attached communities often reported for groundwater environments are not the result of purely stochastic events, but that sediment surfaces select for specific groups of microorganisms that assemble over time in a reproducible, non‐random way.

Anode surface bioaugmentation enhances deterministic biofilm assembly in microbial fuel cells

“…Conversely, in this study, we explored which factors drive biofilm assembly on a pre-colonized surface, which is especially relevant when applying bioaugmentation for in-situ bioremediation of natural environments (Tyagi et al, 2011) or wastewater treatment (Herrero and Stuckey, 2015). In groundwater, it has been shown that the composition of sediment-attached communities can differ substantially compared to suspended planktonic communities (Fillinger et al, 2019; Lehman et al, 2001), therefore, using MFC reactors as a model system allows full control of the environmental conditions and easily differentiating between surface-attached (i.e. anodic biofilm) and suspended communities (Zhang et al, 2019; Zhou et al, 2013).…”

“…the time to reach stable maximal current generation) showed different microbial electroactive communities once in steady state. While most studies focus primarily on biofilm formation on clean surfaces (Brislawn et al, 2019; Fillinger et al, 2019; Zhang et al, 2019; Zhou et al, 2013), here we explored the effect of community assembly processes when the anode surface was pre-colonized (bioaugmented) by a defined electroactive consortium (designated as EDC) on MFC startup. Such pre-colonization is expected to enhance deterministic factors relative to stochastic ones in the formation of the mature, anode biofilm at steady state.…”

Substratum‐associated microbiota

“…Using 16S rRNA amplicon sequencing and shotgun metagenomic approaches, Lau, Zarkasi, Md Sah, and Shu-Chien (2019) investigated microbial communities in the photic and aphotic zones of an aquaculture site and an undisturbed site in a tropical human-made freshwater lake. Fillinger, Zhou, Kellermann, and Griebler (2019) followed the microbial colonization of sterile sediments in microcosms exposed to groundwater in two porous aquifers over a year. Using 16S rRNA amplicon sequencing, the authors showed that sediment surfaces selected for specific groups of microorganisms that assembled over time in a reproducible, non-random way.…”

Distribution of ETBE-degrading microorganisms and functional capability in groundwater, and implications for characterising aquifer ETBE biodegradation potential

“…To our knowledge, no studies have examined the physical location of ETBE-biodegrading activity in an aquifer, that is, the relative contribution of suspended and attached microbial communities to this potential. However, is it known that the taxonomy of attached and suspended microbial communities in aquifers can differ (Alfreider et al 1997;Rizoulis et al 2013;Hug et al 2015;Smith et al 2018;Fillinger et al 2019). Interestingly, several studies have investigated the colonisation of functionally-important GEO-degrading organisms on inert surfaces used in bioreactors (Kharoune 2001;Purswani et al 2011;Hicks et al 2014;Alfonso-Gordillo et al 2016;Guisado et al 2016).…”