Local and Geographic Factors Shape the Occupancy-Frequency Distribution of Freshwater Bacteria

Abstract

Species prevalence across the landscape is related to their local abundance, which is a result of deterministic and stochastic processes that select organisms capable of recolonizing sites where they were once extinct, a process known as the rescue effect. The occupancy-frequency distribution (OFD) describes these patterns and has been extensively used to understand organism's distribution but has been poorly tested on microorganisms. In order to test OFD on freshwater bacteria, we collected data from 60 shallow lakes distributed across a wide area in southeastern Brazil, to determine the bacterial operational taxonomic units (OTUs) that were present in all sites (core) and at only one site (satellite). Then, we analyzed the spatial abundance distributions of individual OTUs to understand the influence of local abundances on regional occupancy patterns. Finally, we tested the environmental factors that influenced occupancy and abundance. We found a significant bimodal OFD for freshwater bacteria using both OTUs (97% clustering) and amplicon sequence variants (ASVs, unique sequences), with 13 core OTUs and 1169 satellite OTUs, but only three core ASVs. Core organisms had a bimodal or gamma abundance distribution. The main driver of the core community was pH, while nutrients were key when the core community was excluded and the rest of the community (mild and satellite taxa) was considered. This study demonstrates the close relationship between local environmental conditions and the abundance and dispersion of microorganisms, which shapes their distribution across the landscape.

Distribution and diversity of anaerobic thermophiles and putative anaerobic nickel-dependent carbon monoxide-oxidizing thermophiles in mesothermal soils and sediments

“…This suggests that communities of both mesophiles and the thermophiles the emerge after heating mesothermal systems are structured by similar phenomena, primarily environmental selection. Nonetheless, occupancy patterns in this study differed in some respects from patterns in other studies of mesophiles ( Chen et al, 2020 ; Lindh et al, 2017 ; Izabel-Shen et al, 2021 ; Mateus-Barros et al, 2021 ; Yan et al, 2021 ). In particular, occupancy in regional scale studies of bacterioplankton in the Baltic Sea ( Lindh et al, 2017 ) and a set of Brazilian lakes ( Mateus-Barros et al, 2021 ) exhibited bimodal patterns with an initial decline in occupancy as site numbers increased followed by an increase in the numbers of ASVs occupying the greatest site numbers.…”

“…Nonetheless, occupancy patterns in this study differed in some respects from patterns in other studies of mesophiles ( Chen et al, 2020 ; Lindh et al, 2017 ; Izabel-Shen et al, 2021 ; Mateus-Barros et al, 2021 ; Yan et al, 2021 ). In particular, occupancy in regional scale studies of bacterioplankton in the Baltic Sea ( Lindh et al, 2017 ) and a set of Brazilian lakes ( Mateus-Barros et al, 2021 ) exhibited bimodal patterns with an initial decline in occupancy as site numbers increased followed by an increase in the numbers of ASVs occupying the greatest site numbers. This distribution has been attributed to the presence of modest numbers of abundant core taxa with traits that permit growth under conditions that prevail at regional scales, along with large numbers of low abundance satellite taxa that grow under more limited conditions.…”

Effects of occupancy estimation on abundance–occupancy relationships

“…Positive abundance–occupancy relationships—the observation that widely distributed species are also more locally abundant—is a general pattern in ecology [1] that has been described for vertebrates [2–4], invertebrates [5–7], plants [8–10] and bacteria [11]. Resource availability [12,13], species niche requirements and dispersal limitation [5,14] are among the mechanisms proposed to explain these positive relationships [12].…”