Nitrotoga is selected over Nitrospira in newly assembled biofilm communities from a tap water source community at increased nitrite loading

Abstract

Community assembly is a central topic in microbial ecology: how do assembly processes interact and what is the relative contribution of stochasticity and determinism? Here, we exposed replicate flow-through biofilm systems, fed with nitrite-supplemented tap water, to continuous immigration from a source community, present in the tap water, to determine the extent of selection and neutral processes in newly assembled biofilm communities at both the community and the functional guild (of nitrite-oxidizing bacteria, NOB) levels. The community composition of biofilms assembled under low and high nitrite loading was described after 40 days of complete nitrite removal. The total community assembly, as well as the NOB guild assembly were largely governed by a combination of deterministic and stochastic processes. Furthermore, we observed deterministic enrichment of certain types of NOB in the biofilms. Specifically, elevated nitrite loading selected for a single Nitrotoga representative, while lower nitrite conditions selected for a number of Nitrospira. Therefore, even when focusing on ecologically coherent ensembles, assembly is the result of complex stochastic and deterministic processes that can only be interrogated by observing multiple assemblies under controlled conditions.

Stochastic processes govern invasion success in microbial communities when the invader is phylogenetically close to resident bacteria

“…Total bacteria were quantified based on 16S rRNA gene copy numbers using the Eubacterial primer set 1055f-1392r as described in Terada et al, [29]. On average 2.5 copies of 16S rRNA gene was estimated per cell, according to rrnDB [30], with the assumption, based on previous work [31], that majority of the community belongs to Gallionellacea and Nitrospiraceae. Nitrospira cells were quantified using Nitrospira-specific qPCR with primer set NTS232f [32] and Nsr1264r [33] targeting the 16 S rRNA genes.…”

“…The primer set Ntoga118F (5′-CTTTCAGCCGGAAA-GAAAACGCA-3′) and Ntoga840R (5′-CTAAG-GAAGTCTCCTCCC-3′) was developed for this study to target the 16S rRNA gene of Nitrotoga cells. The primers were designed based on Nitrotoga amplicon sequences retrieved from a previous experiment where Nitrotoga was enriched from tap water spiked with nitrite [31]. The designed primers cover 27% of known Nitrotoga in the SILVA rRNA database (including that of Nitrotoga HW29) and 100% of the tap water enriched Nitrotoga from previous experiment [31].…”

“…The primers were designed based on Nitrotoga amplicon sequences retrieved from a previous experiment where Nitrotoga was enriched from tap water spiked with nitrite [31]. The designed primers cover 27% of known Nitrotoga in the SILVA rRNA database (including that of Nitrotoga HW29) and 100% of the tap water enriched Nitrotoga from previous experiment [31]. These primers target a 175 bp product that was verified by constructing a clone library of 180 clones, all of which were determined to belong to Nitrotoga genus.…”

“…We enriched 40 resident communities from tap water source community in flow-through microcosms subjected to two nitrite-loading regimes to support the coexistence of competing NOB genera [31]. We described the resident community composition after 60 days of operation (further referred to as initial community) and 14 days after the invasion event (referred to as final community).…”

“…Dispersal can influence the diversity, composition, as well as functioning of a community and the effect of dispersal seems to be enhanced in smaller communities [44]. For NOB guilds newly assembled from tap water, the contribution of dispersal is low, compared to the contribution of selection and drift [31]. Hence, we focus on the relative importance of selection and drift from here on.…”