Hydrologic History Regulates Microbial Biofilm Diversity and Ecosystem Function

Environmental Microbiology · 2026-04-01

Aquatic biofilms are an understudied component of northern peatlands and are expected to play a more prominent role in ecosystem processes in areas where aquatic habitat is expanding. The goal of this study was to investigate how hydrologic history influences biofilm diversity and functional genes. This study was conducted in a long-term water table manipulation that simulates drought (lowered water table treatment) and flooding (raised water table treatment) conditions relative to a control treatment (no manipulation). We used a combination of metabarcoding and metagenomic approaches to (1) examine the diversity of eukaryotic algae, cyanobacteria, bacteria and fungi within the biofilm and (2) identify functional genes associated with alternating wet-dry transitional states. Historical flooding, but not drought, led to broad changes in composition and functional genes, especially those associated with carbon metabolism and nitrogen cycling. Differences were related to changes in relative abundance rather than the presence/absence of individual taxa or genes. Hydrologic history influenced community diversity by reducing interspecific competition or by alleviating resource limitation. These findings show that hydrologic history regulates species membership of the community (and thereby associated genes) but differences in water chemistry and interspecific interactions alter the relative abundance of species and their functional potential.

Ecological constraints and evolutionary trade-offs shape nitrogen fixation across habitats

ISME Communications · 2026-01-01 · 1 citations

Abstract From its earliest beginnings, life’s expansion into new habitats has been profoundly shaped by its reciprocal interactions with a changing Earth. To understand the evolution of life’s metabolic engines, we must therefore uncover the ecological and evolutionary processes that shaped their underlying genes and networks. Here, we focus on nitrogen (N2) fixation, one of life’s most critical metabolisms, and investigate the ecological and evolutionary drivers of complexity within its associated gene machinery. We used a large-scale comparative genomics framework to construct a comprehensive catalog of extant N2 fixation-associated genes and to assess their distribution across diverse microbial genomes and environments. Genomes enriched in N2 fixation genes are generally larger, encode broader metabolic capabilities, span wider habitat ranges, and are predominantly associated with mesophilic and aerobic lifestyles. Evolutionary reconstructions reveal early gene gains in ancestral diazotrophs followed by lineage-specific gene losses in later-diverging taxa, consistent with evolutionary trade-offs driven by changing environments. Together, these findings show that the evolution of N2 fixation is tightly intertwined with the composition and organization of its supporting gene machinery, reflecting feedbacks between genome evolution and shifting environmental and ecological contexts.

Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake

Applied and Environmental Microbiology · 2025-06-20

ABSTRACT The potential for extracellular electron transfer (EET) is a prevailing genomic feature of humic lake bacterioplankton. However, there has been little evidence for the substantial ecological contribution predicted by genetics. We hypothesized that anoxygenic phototrophic electrotrophs and accompanying heterotrophic electrogens cycle dissolved organic matter (DOM) between oxidized and reduced states. We predicted that such bacterioplankton would exhibit diel-scale oscillations due to the light dependency of photosynthesis. Using Trout Bog Lake in Wisconsin, USA, as our model ecosystem, we profiled the water column with depth-discrete metagenomic, physiochemical, and electrochemical analyses. We observed variation in oxidation reduction potential (ORP) in response to sunlight, initiating at depths populated by anoxygenic phototrophs with EET genes. We developed an automated buoy to measure electric current flow between many pairs of electrodes simultaneously, observing correlation in electron consumption to sunlight. Our results, combined with published metatranscriptomic analysis, indicate the occurrence of electron cycling between phototrophic oxidation (electrotrophic metabolism) by Chlorobium and anaerobic respiration (electrogenic metabolism) by Geothrix , involving DOM. We also repeatedly observed gradual seasonal increases in hypolimnion ORP throughout summer. These diel and seasonal patterns imply that electroactive DOM mediates the ecology of electroactive bacteria in lakes, controlling humic lake methane emissions. IMPORTANCE We investigated the physical, chemical, and redox characteristics of a bog lake and electrodes hung therein to test the hypothesis that dissolved organic matter is being cycled between oxidized and reduced states by electroactive bacterioplankton powered by phototrophy. To do so, we performed field-based analyses on multiple timescales using both established and novel instrumentation. We paired these analyses with recently developed bioinformatics pipelines for metagenomics data to investigate genes that enable electroactive metabolism and accompanying metabolisms. Our results are consistent with our hypothesis and yet upend some of our other expectations. Our findings have implications for understanding greenhouse gas emissions from lakes, including electroactivity as an integral part of lake metabolism throughout more of the anoxic parts of lakes and for a longer portion of the summer than expected. Our results also give a sense of what electroactivity occurs at given depths and provide a strong basis for future studies.

Two decades of bacterial ecology and evolution in a freshwater lake

Nature Microbiology · 2025-01-03 · 32 citations

Sulfate Reduction Drives Elevated Methylmercury Formation in the Water Column of a Eutrophic Freshwater Lake

Environmental Science & Technology · 2025-03-28 · 12 citations

formation of MeHg in understudied eutrophic freshwater environments.

Ecological constraints and evolutionary trade-offs shape nitrogen fixation across habitats

bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-20 · 4 citations

Abstract From its earliest beginnings, life’s expansion into new habitats has been profoundly shaped by its reciprocal interactions with Earth’s changing environments. Understanding how ancient metabolisms co-evolved with their environments requires uncovering the ecological and evolutionary processes that structured the functionally linked genes and networks underlying these metabolisms. Here, we focus on nitrogen (N 2 ) fixation, one of life’s most critical metabolisms, and investigate the drivers of complexity in its associated gene machinery today. We used a large-scale comparative genomics framework to construct a comprehensive catalog of extant N 2 fixation-associated genes and assessed their distribution across diverse microbial genomes and environmental backgrounds. Genomes enriched in N 2 fixation genes generally have larger genome sizes, broader metabolic capabilities, wider habitat ranges, and are predominantly associated with mesophilic and aerobic lifestyles. Evolutionary reconstructions reveal a pattern of early gene gains in ancestral diazotrophs followed by lineage-specific gene losses in later diverging taxa, suggesting evolutionary trade-offs shaped by changing environments. These findings demonstrate that the evolution of N 2 fixation has been intertwined with the composition and organization of the genes supporting the overarching N 2 metabolism, driven by feedback between genome evolution and shifting environmental and ecological conditions.

Gender-Based Performance in a Collaborative Learning Engineering Classroom

2025-08-21

Long-Term Euxinia Restricts Microbial Methane Removal in Eutrophic Coastal Basins

Environmental Science & Technology · 2025-10-08

In eutrophic coastal waters, aerobic methane-oxidizing bacteria (MOB) mitigate methane emissions by oxidizing benthic methane even in the stratified, anoxic water column. However, ongoing warming and eutrophication lead to extended stratification periods, enhancing anoxic and sulfidic conditions (euxinia), potentially affecting methane removal capacity. Here we compared overall water column methane removal between sites with irregular, seasonal and longer-term euxinia in the Stockholm Archipelago during summer 2022. The highest water-air methane emissions, bottom water-methane and sulfide accumulation, and the lowest methane oxidation potential were observed under longer-term euxinic bottom water conditions. While MOB relative abundance and potential activity indicated high functioning of the methane biofilter in the seasonally euxinic bottom water layer, the methane-filtering potential was much lower in the longer-term euxinic bottom water. Under persistent euxinic conditions, overall bacterial diversity and microbial network connectivity were lower, likely following a simultaneous shift in redox conditions and a shift toward anaerobic sulfur-cycling. This shift may force MOB to retreat from the euxinic bottom water into the narrow oxycline, reducing the capacity of the methane biofilter and resulting in higher methane emissions. These findings highlight the positive feedback loop that can further amplify oceanic methane emissions, particularly from eutrophic and shallow coastal waters prone to prolonged stratification under global warming.

Unravelling viral ecology and evolution over 20 years in a freshwater lake

Nature Microbiology · 2025-01-03 · 27 citations

OneHealth, Climate Change, and Infectious Microbes

Eos · 2024-01-31

AGU and ASM welcome submissions to a joint special collection focusing on the impacts of climate change and microbes on human well-being.