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

Abstract

Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA‐defined Operational Taxonomic Units, OTUs) across 108 globally‐distributed surface ocean stations. We grouped taxa based on their SpAD shape (“normal‐like”‐ abundant and ubiquitous; “logistic”‐ globally rare, present in few sites; and “bimodal”‐ abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan “normal‐like” OTUs, yet there was a gradual shift towards assemblages dominated by “logistic” taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer “normal‐like” shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members.

Disentangling the mechanisms shaping the surface ocean microbiota

“…Some of these areas correspond to nutrient-rich (selection) coastal zones (the South African Atlantic coast and the South Australia Bight) or potential upwelling (dispersal) zones, such as the Equatorial Pacific and Atlantic as well as the Costa Rica Dome. These findings were coherent with spatial abundance distributions (SpAD) of bacterioplankton in the tropical and subtropical surface-ocean [35]. Altogether, the previous suggests strong selective changes or immigration from deep water layers into the surface associated to upwellings, affecting both prokaryotic and picoeukaryotic community structure.…”

“…Abiotic environmental conditions in adjacent stations over the trajectory of the Malaspina cruise, typically separated by 250-500 km, in the tropical and subtropical ocean (Fig. 1a) are generally comparable [35]. Therefore, compositional differences between pairs of neighbouring communities could manifest the differential capability of distinct microbial assemblages to disperse.…”

Ecogenomics of key prokaryotes in the arctic ocean

“…In line with previous studies 71,73 , the majority of Arctic MAGs (71%) could not be categorized into generalists or specialists, while 21% (n=111) were habitat specialists and 7% (n=38) were generalists ( Figure 6A). High contributions of specialists have been reported in other polar environmental extremes such as coastal Antarctic lakes 70 or in highly productive marine sites compared to oligotrophic open ocean stations 74 . Both generalist and specialist MAGs show a similar range in their mean abundances, which contrasts with lower abundances of specialists in niche breadth analyses of Arctic eukaryotes (Karp-Boss et al, submitted).…”

Rare Species Shift the Structure of Bacterial Communities Across Sphagnum Compartments in a Subalpine Peatland

“…They may become dominant and conduct essential functions in nutrient cycling, which compensate for the function deficiency of abundant species (Jousset et al, 2017) under favorable environmental conditions (Pedrós-Alió, 2007;Aanderud et al, 2015). Additionally, the responses of abundant and rare communities to environmental factors are different (Chen et al, 2017;Ruiz-González et al, 2019) due to the differences in niche breadth, competitiveness of resources and growth rate (Wu et al, 2017;Xue et al, 2018). Previous studies about Sphagnum-associated microbial communities mainly concentrate on abundant taxa, whereas the distribution of rare species among different compartments of Sphagnum (surface peat, ectosphere and endosphere of Sphagnum) still remains largely unknown.…”