Peterse, F. | bioRxiv Science

bioRxiv2026

Isotope Labeling Reveals Complex Microbial Interactions during Agaricus bisporus Compost Colonization

Microbial interactions strongly influence carbon and nitrogen flows in mushroom compost, yet their functional roles during Agaricus bisporus colonization remain unresolved. We combined PLFA-SIP and nanoSIMS imaging with ITS amplicon sequencing to follow resource flows and microbial activity across spatial scales. Stable-isotope tracers (13C-glucose and 15N-ammonium) revealed that A. bisporus simultaneously facilitates and suppresses bacterial populations: fungal activity increased glucose assimilation by bacteria yet reduced overall bacterial biomass. NanoSIMS visualized nutrient-rich microenvironments along hyphae where bacterial 13C and 15N assimilation was elevated. Sequencing showed the fungal community to comprise essentially two organisms, A. bisporus and Mycothermus thermophilus, which differ approximately elevenfold in their content of the fungal biomarker C18:2w6,9c. Total fungal PLFA therefore tracks which of the two dominates as much as it tracks fungal biomass. Together these findings reveal coupled fungal-bacterial nutrient processing and show that biomarker-based estimates of fungal biomass require community composition to be known. Multi-scale isotope probing provides a framework for resolving microbial interactions in complex detrital systems.

microbiology↗

bioRxiv2025

Quantifying spatiotemporal decoupling of GDGT-temperature relationships in a deep alpine lake

Glycerol dialkyl glycerol tetraethers (GDGTs), membrane lipids produced by archaea and some bacteria, are widely used in paleoclimate reconstructions due to their empirical relationship with temperature. However, their application in lakes is complicated by uncertainties in source attribution and environmental controls on their distribution. To address these constraints, we analyzed both branched and isoprenoid GDGTs (brGDGTs and isoGDGTs) in settling particles collected over 19 months using sediment traps at four depths (10, 15, 25 and 35 m) in Lake Lugu, a deep, stratified alpine lake in southwestern China. GDGT fluxes showed synchronous spatiotemporal variations across depths, with higher values during winter mixing than summer stratification, suggesting in situ production enhanced by nutrient upwelling during lake overturn. Correlations between GDGT distributions and high-resolution water temperature profiles revealed strong temperature sensitivity in isoGDGTs, particularly the Ring Index (RI), with peak correlations linked to mean temperatures [~]20 days prior to trap recovery, indicating a clear temporal lag in GDGT-temperature relationship. Moreover, stronger correlations with temperatures at overlying depths, implying vertical transport of isoGDGTs and a dominant autochthonous origin from the upper water column. In contrast, brGDGTs displayed weak or non-significant temperature dependence, likely reflecting distinct microbial sources or other controlling factors. These findings underscore the utility of isoGDGT-based proxies, particularly RI, while highlighting the importance of accounting for spatiotemporal offsets in GDGTs production when reconstructing paleotemperatures in deep, stratified lakes.

ecology↗