Deterministic processes drive national‐scale patterns in lake surface sediment bacteria and eukaryotic assemblage composition

Pearman, John K.; Adamson, Janet; Thomson‐Laing, Georgia; Thompson, L. M.; Waters, Sean; Vandergoes, Marcus J.; Howarth, Jamie; Wood, Susanna A.

doi:10.1002/lno.12247

Cited by 5 publications

(5 citation statements)

References 78 publications

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“…Community similarity and the percent of shared ESVs between communities declined substantially among lakes regardless of whether the lake was 5 or 400 km apart (Figures 5 and S5A–C). Similarly, Pearman and others (Pearman, Adamson, et al, 2022) found 54% of bacterial taxa in lake surface sediments were observed only in a single lake. However, once microbes are buried into deeper sediment layers, we observed a high degree of selection for closely related communities, particularly in the depauperate zone (Figure 6B, C).…”

Section: Discussionmentioning

confidence: 99%

“…Our results agree with analyses of microbial communities within the surface sediments (first few cm) of lakes in other regions. In these studies, variable selection, driven by environmental differences, created differences among communities (Jiao et al, 2021; Pearman et al 2022, b; Xia et al, 2022; Yang et al, 2020; Zeng et al, 2019). Specifically, water nutrients, algal concentrations, and pH have been suggested to cause a strong selection of sediment bacteria (Jiao et al, 2021; Pearman, Adamson, et al, 2022; Zeng et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…In these studies, variable selection, driven by environmental differences, created differences among communities (Jiao et al, 2021; Pearman et al 2022, b; Xia et al, 2022; Yang et al, 2020; Zeng et al, 2019). Specifically, water nutrients, algal concentrations, and pH have been suggested to cause a strong selection of sediment bacteria (Jiao et al, 2021; Pearman, Adamson, et al, 2022; Zeng et al, 2019). Consistent with these studies, we observed strong environmental selection across our dataset (Figure 6B,C), although understanding the specific lake parameters or sediment characteristics involved will require further study.…”

Section: Discussionmentioning

confidence: 99%

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Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes

Von Eggers,

Wisnoski,

Calder

et al. 2024

Environmental Microbiology

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Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low‐energy adapted taxa in deeper zones. Stochastic processes—like dispersal limitation—contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes

Von Eggers,

Wisnoski,

Calder

et al. 2024

Environmental Microbiology

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“…On the other hand, stochastic processes or some uninvestigated important environmental variables might contribute to the patterns of the PMA‐treated protistan and fungal communities (Wang et al, 2020). Additionally, deterministic processes may be more important for bacteria than eukaryotes in some freshwater systems (Pearman et al, 2022; Wan et al, 2023). Collectively, relic DNA remaining in waters can obscure the relationships between microbial taxa and environmental conditions.…”

Section: Discussionmentioning

confidence: 99%

Relic DNA obscures DNA‐based profiling of multiple microbial taxonomic groups in a river‐reservoir ecosystem

Xue

Chen

et al. 2023

Molecular Ecology

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Numerous studies have investigated the spatiotemporal variability in water microbial communities, yet the effects of relic DNA on microbial community profiles, especially microeukaryotes, remain far from fully understood. Here, total and active bacterial and microeukaryotic community compositions were characterized using propidium monoazide (PMA) treatment coupled with high‐throughput sequencing in a river‐reservoir ecosystem. Beta diversity analysis showed a significant difference in community composition between both the PMA untreated and treated bacteria and microeukaryotes; however, the differentiating effect was much stronger for microeukaryotes. Relic DNA only resulted in underestimation of the relative abundances of Bacteroidota and Nitrospirota, while other bacterial taxa exhibited no significant changes. As for microeukaryotes, the relative abundances of some phytoplankton (e.g. Chlorophyta, Dinoflagellata and Ochrophyta) and fungi were greater after relic DNA removal, whereas Cercozoa and Ciliophora showed the opposite trend. Moreover, relic DNA removal weakened the size and complexity of cross‐trophic microbial networks and significantly changed the relationships between environmental factors and microeukaryotic community composition. However, there was no significant difference in the rates of temporal community turnover between the PMA untreated and treated samples for either bacteria or microeukaryotes. Overall, our results imply that the presence of relic DNA in waters can give misleading information of the active microbial community composition, co‐occurrence networks and their relationships with environmental conditions. More studies of the abundance, decay rate and functioning of nonviable DNA in freshwater ecosystems are highly recommended in the future.

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“…However, deterministic processes dominate bacterial community assembly in the Paran a River (Huber et al, 2020). Whether stochasticity and/or determinism dominating planktonic community assembly seems to be influenced by geospatial differences and environmental heterogeneity (Huber et al, 2020;Pearman et al, 2022).…”

Section: Distinct Divergence In Diversity Maintenance Between Bacteri...mentioning

confidence: 99%

Abundance and diversity of eukaryotic rather than bacterial community relate closely to the trophic level of urban lakes

Wan

Gadd

et al. 2022

Environmental Microbiology

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Scientific understanding of biotic effects on the water trophic level is lacking for urban lakes during algal bloom development stage. Based on the Illumina MiSeq sequencing, quantitative polymerase chain reaction (PCR), and multiple statistical analyses, we estimated distribution patterns and ecological roles of planktonic bacteria and eukaryotes in urban lakes during algal bloom development stage (i.e., April, May, and June). Cyanobacteria and Chlorophyta mainly dominated algal blooms. Bacteria exhibited significantly higher absolute abundance and community diversity than eukaryotes, whereas abundance and diversity of eukaryotic rather than bacterial community relate closely to the water trophic level. Multinutrient cycling (MNC) index was significantly correlated with eukaryotic diversity rather than bacterial diversity. Stronger species replacement, broader environmental breadth, and stronger phylogenetic signal were found for eukaryotic community than for bacterial community. In contrast, bacterial community displayed stronger community stability and environmental constraint than eukaryotic community. Stochastic and differentiating processes contributed more to community assemblies of bacteria and eukaryotes. Our results emphasized that a strong linkage between planktonic diversity and MNC ensured a close relationship between planktonic diversity and the water trophic level of urban lakes. Our findings could be useful to guide the formulation and implementation of environmental lake protection measures.

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Deterministic processes drive national‐scale patterns in lake surface sediment bacteria and eukaryotic assemblage composition

Cited by 5 publications

References 78 publications

Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes

Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes

Relic DNA obscures DNA‐based profiling of multiple microbial taxonomic groups in a river‐reservoir ecosystem

Abundance and diversity of eukaryotic rather than bacterial community relate closely to the trophic level of urban lakes

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