Abstract:Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomas… Show more
“…In our system, labile DOC in GW may also be indirectly derived from methanotrophy, as methane concentrations are elevated within fine-grained sediments that underlie the coarse-grained sediments within which we sampled 28 . Labile DOC in the GW of our system may also be leached from buried organic carbon deposits (e.g., woody material), which occur sporadically in the aquifer 29 . Fig.…”
The hyporheic corridor (HC) encompasses the river–groundwater continuum, where the mixing of groundwater (GW) with river water (RW) in the HC can stimulate biogeochemical activity. Here we propose a novel thermodynamic mechanism underlying this phenomenon and reveal broader impacts on dissolved organic carbon (DOC) and microbial ecology. We show that thermodynamically favorable DOC accumulates in GW despite lower DOC concentration, and that RW contains thermodynamically less-favorable DOC, but at higher concentrations. This indicates that GW DOC is protected from microbial oxidation by low total energy within the DOC pool, whereas RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW–RW mixing overcomes these protections and stimulates respiration. Mixing models coupled with geophysical and molecular analyses further reveal tipping points in spatiotemporal dynamics of DOC and indicate important hydrology–biochemistry–microbial feedbacks. Previously unrecognized thermodynamic mechanisms regulated by GW–RW mixing may therefore strongly influence biogeochemical and microbial dynamics in riverine ecosystems.
“…In our system, labile DOC in GW may also be indirectly derived from methanotrophy, as methane concentrations are elevated within fine-grained sediments that underlie the coarse-grained sediments within which we sampled 28 . Labile DOC in the GW of our system may also be leached from buried organic carbon deposits (e.g., woody material), which occur sporadically in the aquifer 29 . Fig.…”
The hyporheic corridor (HC) encompasses the river–groundwater continuum, where the mixing of groundwater (GW) with river water (RW) in the HC can stimulate biogeochemical activity. Here we propose a novel thermodynamic mechanism underlying this phenomenon and reveal broader impacts on dissolved organic carbon (DOC) and microbial ecology. We show that thermodynamically favorable DOC accumulates in GW despite lower DOC concentration, and that RW contains thermodynamically less-favorable DOC, but at higher concentrations. This indicates that GW DOC is protected from microbial oxidation by low total energy within the DOC pool, whereas RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW–RW mixing overcomes these protections and stimulates respiration. Mixing models coupled with geophysical and molecular analyses further reveal tipping points in spatiotemporal dynamics of DOC and indicate important hydrology–biochemistry–microbial feedbacks. Previously unrecognized thermodynamic mechanisms regulated by GW–RW mixing may therefore strongly influence biogeochemical and microbial dynamics in riverine ecosystems.
“…Community assembly processes operate over space and time and influence community structure and eventually microbial metabolisms (Graham, Knelman, et al, ). So far, attempts have been made to understand these processes in a broad range of biomes such as recently deglaciated soils (Castle et al, ; Nemergut et al, ), lake biofilms (Jackson et al, ), water pipes (Martiny et al, ), river sediments (Graham, Crump, et al, ; Stegen, Fredrickson, et al, ; Stegen, Konopka, et al, ; Stegen et al, , ), subseafloor sediments (Starnawski et al, ), and global desert soils (Caruso et al, ). Our study examined a unique system where community assembly processes in an incipient terrestrial system were assessed in a highly controlled and spatially explicit manner.…”
Microbial dynamics drive the biotic machinery of early soil evolution. However, integrated knowledge of microbial community establishment, functional associations, and community assembly processes in incipient soil is lacking. This study presents a novel approach of combining microbial phylogenetic profiling, functional predictions, and community assembly processes to analyze drivers of microbial community establishment in an emerging soil system. Rigorous submeter sampling of a basalt-soil lysimeter after 2 years of irrigation revealed that microbial community colonization patterns and associated soil parameters were depth dependent. Phylogenetic analysis of 16S rRNA gene sequences indicated the presence of diverse bacterial and archaeal phyla, with high relative abundance of Actinomyceles on the surface and a consistently high abundance of Proteobacteria (Alpha, Beta, Gamma, and Delta) at all depths. Despite depth-dependent variation in community diversity, predicted functional gene analysis suggested that microbial metabolisms did not differ with depth, thereby suggesting redundancy in functional potential throughout the system. Null modeling revealed that microbial community assembly patterns were predominantly governed by variable selection. The relative influence of variable selection decreased with depth, indicating unique and relatively harsh environmental conditions near the surface and more benign conditions with depth. Additionally, community composition near the center of the domain was influenced by high levels of dispersal, suggesting that spatial processes interact with deterministic selection imposed by the environment. These results suggest that for oligotrophic systems, there are major differences in the length scales of variation between vertical and horizontal dimensions with the vertical dimension dominating variation in physical, chemical, and biological features.Citation:
“…Nevertheless, our results fit observations on assembly processes for communities in the hyporheic zone (Graham et al, 2016b;Stegen et al, 2016a;2018) as well as biofilms in surface water streams (Besemer et al, 2012;Veach et al, 2016), suggesting that selection not only plays a determining role in the assembly of surface-attached microbial communities in those dynamic environments but also in pristine groundwater aquifers, despite the comparatively more stable environmental conditions, which have been shown to promote the effect of stochastic over deterministic processes in other environments (Ofiţeru et al, 2010;Stegen et al, 2012;Wang et al, 2013;Zhou et al, 2013). Mineral composition has previously been demonstrated to be a driving factor for microbial community composition and assembly (Grösbacher et al, 2016;Stegen et al, 2016b;Jones and Bennett, 2017). Since the in situ microcosms that we incubated at the two sites in our study were filled with sediment that originated from the same source, it is likely that identical sediment properties selected for the highly similar microbial communities at the two sites.…”
Section: Discussionmentioning
confidence: 99%
“…To date, most of the studies on ecological processes behind the assembly of microbial communities in groundwater environments have focused on planktonic communities suspended in the groundwater (Stegen et al, 2012;Beaton et al, 2016;Danczak et al, 2018), while studies on sediment-attached communities are scarce (Stegen et al, 2016b). In contrast, much insight has been gained over the past years into the assembly of sediment-attached communities in groundwater-surface water mixing zones (hyporheic zone).…”
Summary
Sediments accommodate the dominating share of groundwater microbiomes, however the processes that govern the assembly and succession of sediment‐attached microbial communities in groundwater aquifers are not well understood. To elucidate these processes, we followed the microbial colonization of sterile sediments in in situ microcosms that were exposed to groundwater for almost 1 year at two distant but hydrologically connected sites of a pristine, shallow, porous aquifer. Our results revealed intriguing similarities between the community succession on the newly‐colonized sediments and succession patterns previously observed for biofilms in other more dynamic aquatic environments, indicating that the assembly of microbial communities on surfaces may be governed by similar underlying mechanisms across a wide range of different habitats. Null model simulations on spatiotemporally resolved 16S rRNA amplicon sequencing data further indicated selection of specific OTUs rather than random colonization as the main driver of community assembly. A small fraction of persistent OTUs that had established on the sediments during the first 115 days dominated the final communities (68%–85%), suggesting a key role of these early‐colonizing organisms, in particular specific genera within the Comamonadaceae and Oxalobacteraceae, for community assembly and succession during the colonization of the sediments. Overall, our study suggests that differences between planktonic and sediment‐attached communities often reported for groundwater environments are not the result of purely stochastic events, but that sediment surfaces select for specific groups of microorganisms that assemble over time in a reproducible, non‐random way.
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