Identifying the core seed bank of a complex boreal bacterial metacommunity

Abstract

Seed banks are believed to contribute to compositional changes within and across microbial assemblages, but the application of this concept to natural communities remains challenging. Here we describe the core seed bank of a bacterial metacommunity from a boreal watershed, using the spatial distribution of bacterial operational taxonomic units (OTUs) across 223 heterogeneous terrestrial, aquatic and phyllosphere bacterial assemblages. Taxa were considered potential seeds if they transitioned from rare to abundant somewhere within the metacommunity and if they were ubiquitous and able to persist under unfavorable conditions, the latter assessed by checking their presence in three deeply sequenced samples (one soil, one river and one lake, 2.2-3 million reads per sample). We show that only a small fraction (13%) of all detected OTUs constitute a metacommunity seed bank that is shared between all terrestrial and aquatic communities, but not by phyllosphere assemblages, which seem to recruit from a different taxa pool. Our results suggest directional recruitment driven by the flow of water in the landscape, since most aquatic sequences were associated to OTUs found in a single deeply-sequenced soil sample, but only 45% of terrestrial sequences belonged to OTUs found in the two deeply-sequenced aquatic communities. Finally, we hypothesize that extreme rarity, and its interplay with water residence time and growth rates, may further constrain the size of the potential seed bank.

Contrasting dynamics and environmental controls of dispersed bacteria along a hydrologic gradient

“…Therefore, the fact that those OTUs present across the sampled headwaters included taxa that would become dominant in all of the larger rivers suggests that there must be a large regional pool of taxa from which aquatic communities recruit, which is not subjected to dispersal limitation. Interestingly, this idea of the landscape reservoir of aquatic diversity has been proposed at scales much larger than the present study (Niño-García et al, 2016a;Ruiz-González et al, 2015a, 2017 and is in accordance with the seed-bank concept, a standing reservoir of dormant microbes (i.e., microbes in a reversible state of very low metabolic activity) that persist at low abundances but that can grow and become abundant upon changes in environmental conditions (Lennon and Jones, 2011). This further highlights that microbial seed banks may transcend ecosystem types, such that viable microbes can persist under unfavourable conditions in some ecosystems until they are transported to a suitable environment (Sjöstedt et al, 2012;Lee et al, 2013;Comte et al, 2014;Ruiz-González et al, 2015a, 2017.…”

Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean

“…Second, prokaryotes can be dispersed much longer distances and can persist out of their suitable niches (dormant or inactive but capable of resuming growth, Lennon & Jones, ) for longer times than larger organisms (Langenheder et al, ; Sebastián et al, ). This, coupled to the fact that our perception of taxa occurrence is largely dependent on the sequencing resolution (Gibbons et al, ; Ruiz‐González et al, ), explains why our understanding of the ecology and mechanisms associated with microbial cosmopolitanism, dominance or rarity is far behind that of macroorganisms. In this context, the identification of bacterial spatial “behaviours” across large spatial scales is emerging as a promising way to gain insight into microbial biogeography drivers (Mestre et al, ; Niño‐García et al, ; Ruiz‐González et al, , ).…”

“…This, coupled to the fact that our perception of taxa occurrence is largely dependent on the sequencing resolution (Gibbons et al, ; Ruiz‐González et al, ), explains why our understanding of the ecology and mechanisms associated with microbial cosmopolitanism, dominance or rarity is far behind that of macroorganisms. In this context, the identification of bacterial spatial “behaviours” across large spatial scales is emerging as a promising way to gain insight into microbial biogeography drivers (Mestre et al, ; Niño‐García et al, ; Ruiz‐González et al, , ). For example, the SpAD approach allowed discovering that hydrologic transport from rivers explained the presence of most rare bacteria in boreal lakes, but at the same time inoculated taxa able to thrive in lake conditions (Niño‐García et al, ).…”

“…Some studies have linked the ubiquity of taxa to their genomic content and metabolic versatility, showing that whereas the most ubiquitous bacteria in the surface oligotrophic ocean have simplified and streamlined genomes (Lauro et al, ; Swan et al, ), those from soils show large genomes and high metabolic versatility (Barberán et al, ). Also, the widespread distribution of certain prokaryotes has been associated with their capacity to persist in unfavourable conditions upon dispersal (i.e., as dormant or spores, as suggested by Hubert et al, ; Ruiz‐González et al, ; Mestre et al, ). However, little is known about how cosmopolitan or rare taxa assemble to constitute communities, and whether environmental transitions or dispersal barriers promote shifts in their abundances.…”

Large‐scale biogeography and environmental regulation of methanotrophic bacteria across boreal inland waters

“…In this study, we combined the data sets previously published in Niño‐García, Ruiz‐González, and del Giorgio () and in Ruiz‐González, Niño‐García, Kembel, and del Giorgio (), and Ruiz‐González, Niño‐García, and del Giorgio (). This combined data set consists of 705 environmental samples (302 lakes, 316 rivers, 43 soil waters and 44 soils) collected between 2009 and 2013 from seven different regions in Québec (Canada): Abitibi, Baie‐James, Chibougameau, Saguenay, Côte‐Nord, Laurentides and Schefferville (Figure ).…”