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ABSTRACT Dead fungal cells, known as necromass, are increasingly recognised as significant contributors to long‐term soil carbon pools, yet the genes involved in necromass decomposition are poorly understood. In particular, how microorganisms degrade necromass with differing initial cell wall chemical compositions using carbohydrate‐active enzymes (CAZymes) has not been well studied. Based on the frequent occurrence and high abundance of the fungal genusTrichodermaon decaying fungal necromass in situ, we grewTrichoderma reeseiRUT‐C30 on low and high melanin necromass ofHyaloscypha bicolor(Ascomycota) in liquid cultures and assessedT. reeseigene expression relative to each other and relative to glucose. Transcriptome data revealed thatT. reeseiup‐regulated many genes (over 100; necromass versus glucose substrate) coding for CAZymes, including enzymes that would target individual layers of an Ascomycota fungal cell wall. We also observed differential expression of protease‐ and laccase‐encoding genes on high versus low melanin necromass, highlighting a subset of genes (fewer than 15) possibly linked to the deconstruction of melanin, a cell wall constituent that limits necromass decay rates in nature. Collectively, these results advance our understanding of the genomic traits underpinning the rates and fates of carbon turnover in an understudied pool of Earth's belowground carbon, fungal necromass. 

Abstract Organic sulfur plays a crucial role in the biogeochemistry of aquatic sediments, especially in low sulfate (< 500 μM) environments like freshwater lakes and the Earth's early oceans. To better understand organic sulfur cycling in these systems, we followed organic sulfur in the sulfate‐poor (< 40 μM) iron‐rich (30–80 μM) sediments of Lake Superior from source to sink. We identified microbial populations with shotgun metagenomic sequencing and characterized geochemical species in porewater and solid phases. In anoxic sediments, we found an active sulfur cycle fueled primarily by oxidized organic sulfur. Sediment incubations indicated a microbial capacity to hydrolyze sulfonates, sulfate esters, and sulfonic acids to sulfate. Gene abundances for dissimilatory sulfate reduction (dsrAB) increased with depth and coincided with sulfide maxima. Despite these indicators of sulfide formation, sulfide concentrations remain low (< 40 nM) due to both pyritization and organic matter sulfurization. Immediately below the oxycline, pyrite accounted for 13% of total sedimentary sulfur. Both free and intact lipids in this same interval accumulated disulfides, indicating rapid sulfurization even at low concentrations of sulfide. Our investigation revealed a new model of sulfur cycling in a low‐sulfate environment that likely extends to other modern lakes and possibly the ancient ocean, with organic sulfur both fueling sulfate reduction and consuming the resultant sulfide.