Understanding stochastic and deterministic assembly processes in microbial communities along temporal, spatial and environmental scales

Abstract

The mechanisms driving community assembly have been repeatedly studied as one of the major questions in ecology (Legendre

Different Microeukaryotic Trophic Groups Show Different Latitudinal Spatial Scale Dependences in Assembly Processes across the Continental Shelves of China

“…As spatial scale increased, several factors contributed to the greater effects of dispersal limitation and heterogeneous selection for microorganisms. These factors included the failure of microbial establishment, increased environmental heterogeneity, and the influence of different currents [ 9 , 17 , 69 ]. Surprisingly, we found that the variation in assembly processes within planktonic communities was primarily influenced by temperature rather than latitude and geographical distance.…”

“…Speciation, the evolution of new species, is not considered due to its relatively limited impact on the metacommunities and the considerable challenges associated with measurement in natural environments [ 6 , 7 , 8 ]. Recently, unraveling the relative contribution of deterministic and stochastic processes could enable significant progress in understanding the community assembly [ 9 ]. However, previous studies have reported that the relative contribution of each process varies across different spatiotemporal scales [ 10 , 11 , 12 ].…”

Editorial 2024

“…Finally, our third Special Issue, Insights into Ecological & Evolutionary Processes via Community Metabarcoding includes ‘papers that highlight the power of high‐throughput sequencing (HTS) data to address classic questions in ecology and evolution, particularly focused on metabarcoding (amplicon) datasets in conjunction with complementary ‐omics data types and/or models/theory to infer overall ecosystem processes’ (Gillespie et al., 2023). The impressive collection of 44 manuscripts covers a wide range of topics: community assembly processes (Andujar et al., 2022; Arjona et al., 2022; Emerson et al., 2022; Govender et al., 2022; Guerrieri et al., 2022; Ip, Chang, Oh, et al., 2022; Kiemel et al., 2022; Li et al., 2022; Macheriotou et al., 2023; Menéndez‐Serra et al., 2023; Nappi et al., 2022; Noguerales et al., 2023; Overcast et al., 2023; Pino et al., 2023; Van der Loos et al., 2022; Wang et al., 2022), interaction networks (Ando et al., 2022; Bell et al., 2022; Dürrbaum et al., 2022; Encinas‐Viso et al., 2022; Ficetola & Taberlet, 2023; Graham et al., 2022; Ip, Chang, Tun, et al., 2022; Lowe et al., 2022; Lu et al., 2022; Lue et al., 2022; Pitteloud et al., 2022; Srivathsan et al., 2022; Tommasi et al., 2022), cross‐scale interactions and microbiomes (Brinker et al., 2022; Câmara dos Reis et al., 2022; Hu et al., 2022; Kivistik et al., 2022; Manthey et al., 2022; Merges et al., 2022; Michel et al., 2022; Molina et al., 2022; Navine et al., 2022; Pereira et al., 2022; Perez‐Lamarque & Morlon, 2022; Rolshausen et al., 2022), and invasive species/homogenization (Andrés et al., 2023; Graham et al., 2022; Hampel et al., 2022; Kennedy et al., 2022; Overcast et al., …”

“…Collectively the articles in this Special Issue 'underline the huge impact of the anthropogenic environment in microbial evolution, including the emergence and spread of pathogens as well as the benefits provided by domesticated or mutualistic fungi and bacteria'(Giraud et al, 2023).Finally, our third Special Issue, Insights into Ecological & Evolutionary Processes via Community Metabarcoding includes 'papers that highlight the power of high-throughput sequencing (HTS) data to address classic questions in ecology and evolution, particularly focused on metabarcoding (amplicon) datasets in conjunction with complementary -omics data types and/or models/theory to infer overall ecosystem processes'(Gillespie et al, 2023). The impressive collection of 44 manuscripts covers a wide range of topics: community assembly processes(Andujar et al, 2022;Arjona et al, 2022;Emerson et al, 2022;Govender et al, 2022;Guerrieri et al, 2022;Ip, Chang, Oh, et al, 2022;Kiemel et al, 2022;Li et al, 2022;Macheriotou et al, 2023;Menéndez-Serra et al, 2023;Nappi et al, 2022;Noguerales et al, 2023;Overcast et al, 2023;Pino et al, 2023;Van der Loos et al, 2022;Wang et al, 2022), interaction networks(Ando et al, 2022;Bell et al, 2022;Dürrbaum et al, 2022;Encinas-Viso et al, 2022;Ficetola & Taberlet, 2023;Graham et al, 2022;Ip, Chang, Tun, et al, 2022;Lowe et al, 2022;Lu et al, 2022;Lue et al, 2022;Pitteloud et al, 2022;Srivathsan et al, 2022;Tommasi et al, 2022), cross-scale interactions and microbiomes(Brinker et al, 2022;Câmara dos Reis et al, 2022...…”

Insights into Ecological & Evolutionary Processes via community metabarcoding

“…Biodiversity-the multiplicity of life, from microbes to macro-organisms and from genes to ecosystems-is in crisis, yet we have little understanding of factors that can sustain biodiversity and enhance its resilience to perturbations (IPBES, 2019;Oliver et al, 2015). Key questions that remain include the interplay between niche and neutral processes in shaping the assembly of communities (Mittelbach & McGill, 2019) and the associated role of stochastic and deterministic processes governing assembly (Menéndez-Serra et al, 2023); the complexity-stability paradox (Domínguez-García et al, 2019); metacommunity dynamics and the connection between local and regional diversity (Thompson et al, 2020); the extent to which a given community can exist in equilibrium or steady state (Qian & Akçay, 2020) and concepts of alternative stable states (Van Nes et al, 2016), among others. These questions have been the focus of much theoretical development in the past, but the ability to generate the data needed to validate these theories has been limited by the difficulty of sampling biological communities at the needed scale.…”