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1. The dynamics of cable bacteria colonization in surface sediments: a 2D view

   https://doi.org/10.1038/s41598-021-86365-1  

   Yin, Hang; Aller, Robert C.; Zhu, Qingzhi; Aller, Josephine Y. (December 2021, Scientific Reports)

   null (Ed.)

   Abstract Cable bacteria that are capable of transporting electrons on centimeter scales have been found in a variety of sediment types, where their activity can strongly influence diagenetic reactions and elemental cycling. In this study, the patterns of spatial and temporal colonization of surficial sediment by cable bacteria were revealed in two-dimensions by planar pH and H 2 S optical sensors for the first time. The characteristic sediment surface pH maximum zones begin to develop from isolated micro-regions and spread horizontally within 5 days, with lateral spreading rates from 0.3 to ~ 1.2 cm day −1 . Electrogenic anodic zones in the anoxic sediments are characterized by low pH, and the coupled pH minima also expand with time. H 2 S heterogeneities in accordance with electrogenic colonization are also observed. Cable bacteria cell abundance in oxic surface sediment (0–0.25 cm) kept almost constant during the colonization period; however, subsurface cell abundance apparently increased as electrogenic activity expanded across the entire surface. Changes in cell abundance are consistent with filament coiling and growth in the anodic zone (i.e., cathodic snorkels). The spreading mechanism for the sediment pH–H 2 S fingerprints and the cable bacteria abundance dynamics suggest that once favorable microenvironments are established, filamentous cable bacteria aggregate or locally activate electrogenic metabolism. Different development dynamics in otherwise similar sediment suggests that the accessibility of reductant (e.g., dissolved phase sulfide) is critical in controlling the growth of cable bacteria. 

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2. Worm tubes as conduits for the electrogenic microbial grid in marine sediments

   https://doi.org/10.1126/sciadv.aaw3651  

   Aller, Robert C.; Aller, Josephine Y.; Zhu, Qingzhi; Heilbrun, Christina; Klingensmith, Isaac; Kaushik, Aleya (July 2019, Science Advances)

   Electrogenic cable bacteria can couple spatially separated redox reaction zones in marine sediments using multicellular filaments as electron conductors. Reported as generally absent from disturbed sediments, we have found subsurface cable aggregations associated with tubes of the parchment worm Chaetopterus variopedatus in otherwise intensely bioturbated deposits. Cable bacteria tap into tubes, which act as oxygenated conduits, creating a three-dimensional conducting network extending decimeters into sulfidic deposits. By elevating pH, promoting Mn, Fe-oxide precipitation in tube linings, and depleting S around tubes, they enhance tube preservation and favorable biogeochemical conditions within the tube. The presence of disseminated filaments a few cells in length away from oxygenated interfaces and the reported ability of cable bacteria to use a range of redox reaction couples suggest that these microbes are ubiquitous facultative opportunists and that long filaments are an end-member morphological adaptation to relatively stable redox domains. 

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3. Biogeochemical plumbing of pioneer mangrove intertidal flats in French Guiana

   Aller, R; Klingensmith, I; Stieglitz, T; Heilbrun, C; Waugh, S; Aschenbroich, A; Thouzeau, G; Michaud, E (July 2024, Regional Environmental Change)

   Reyer, C (Ed.)

   Migrating mudbanks are characteristic features of the vast Amazon-Guianas coastline along Northeastern South America. As illustrated by sites in French Guiana, consolidating mudfats that periodically transition to mangrove forest are permeated by extensive crustacean burrow systems, sometimes in isolation but more often in close association with morpho-sedimentary structures such as tidal pools and channels. Burrow structures are critical to mangrove growth. In this study, we evaluated the ways in which burrows act as complex conduits that plumb deposits for solute exchange with overlying water. We sampled burrows during low tide when irrigation is inhibited and burrow water rapidly becomes anoxic. The products of diagenetic reactions, for example: NH4+, N2, and Si(OH)4, build up with time, revealing sedimentary reaction rates and fluxes. When oxygenated, burrow walls are zones of intense coupled redox reactions such as nitrification-denitrifcation. Build-up often is lower in burrows connected directly to tidal pools where photosynthetic activity consumes remineralized nutrients, and burrows can remain periodically irrigated at low tide. During food, burrows, particularly those that connect tidal pools laterally to channels, can be rapidly flushed and oxygenated as channel water rises and then spreads across flats. Burrow flushing produces enhanced concentrations of nutrients within the leading edge of the flood as seawater moves progressively towards and into adjacent mangroves. Estimates of burrow volumes obtained from drone surveys together with burrow solute production rates allow upscaling of burrow-sourced metabolite fluxes; however, these are extremely variable due to variable burrow geometries, connections between burrows, pools, and channels, and burrow water residence times (oxygenation). The flushing of burrows during food results in a rectification of sediment-water fluxes shoreward and enhances the delivery of nutrients from the flats into adjacent mangroves and pools, presumably stimulating colonization and forest growth. 

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4. Bioindicator “fingerprints” of methane-emitting thermokarst features in Alaskan soils

   https://doi.org/10.3389/fmicb.2024.1462941  

   Smallwood, Chuck R; Hasson, Nicholas; Yang, Jihoon; Schambach, Jenna; Bennett, Haley; Ricken, Bryce; Sammon, Jason; Mascarenas, Monica; Eberling, Naomi; Kolker, Stephanie; et al (February 2025, Frontiers in Microbiology)

   Permafrost thaw increases the bioavailability of ancient organic matter, facilitating microbial metabolism of volatile organic compounds (VOCs), carbon dioxide, and methane (CH₄). The formation of thermokarst (thaw) lakes in icy, organic-rich Yedoma permafrost leads to high CH₄emissions, and subsurface microbes that have the potential to be biogeochemical drivers of organic carbon turnover in these systems. However, to better characterize and quantify rates of permafrost changes, methods that further clarify the relationship between subsurface biogeochemical processes and microbial dynamics are needed. In this study, we investigated four sites (two well-drained thermokarst mounds, a drained thermokarst lake, and the terrestrial margin of a recently formed thermokarst lake) to determine whether biogenic VOCs (1) can be effectively collected during winter, and (2) whether winter sampling provides more biologically significant VOCs correlated with subsurface microbial metabolic potential. During the cold season (March 2023), we drilled boreholes at the four sites and collected cores to simultaneously characterize microbial populations and captured VOCs. VOC analysis of these sites revealed “fingerprints” that were distinct and unique to each site. Total VOCs from the boreholes included > 400 unique VOC features, including > 40 potentially biogenic VOCs related to microbial metabolism. Subsurface microbial community composition was distinct across sites; for example, methanogenic archaea were far more abundant at the thermokarst site characterized by high annual CH₄emissions. The results obtained from this method strongly suggest that ∼10% of VOCs are potentially biogenic, and that biogenic VOCs can be mapped to subsurface microbial metabolisms. By better revealing the relationship between subsurface biogeochemical processes and microbial dynamics, this work advances our ability to monitor and predict subsurface carbon turnover in Arctic soils. 

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5. Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation

   Mara, P.; Zhou, Y.; Teske, A.; Morono, Y.; Beaudoin, D.; Edgcomb, V. (September 2023, The ISME journal)

   Analyses of gene expression of subsurface bacteria and archaea provide insights into their physiological adaptations to in situ subsurface conditions. We examined patterns of expressed genes in hydrothermally heated subseafloor sediments with distinct geochemical and thermal regimes in Guaymas Basin, Gulf of California, Mexico. RNA recovery and cell counts declined with sediment depth, however, we obtained metatranscriptomes from eight sites at depths spanning between 0.8 and 101.9m below seafloor. We describe the metabolic potential of sediment microorganisms, and discuss expressed genes involved in tRNA, mRNA, and rRNA modifications that enable physiological flexibility of bacteria and archaea in the hydrothermal subsurface. Microbial taxa in hydrothermally influenced settings like Guaymas Basin may particularly depend on these catalytic RNA functions since they modulate the activity of cells under elevated temperatures and steep geochemical gradients. Expressed genes for DNA repair, protein maintenance and circadian rhythm were also identified. The concerted interaction of many of these genes may be crucial for microorganisms to survive and to thrive in the Guaymas Basin subsurface biosphere. 

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