Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study

Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective

Terrestrial and aquatic ecosystems have specific carbon fingerprints and sequestration potential, due to the intrinsic properties of the organic matter (OM), mineral content, environmental conditions, and microbial community composition and functions. A small variation in the OM pool can imbalance the carbon dynamics that ultimately affect the climate and functionality of each ecosystem, at regional and global scales. Here, we review the factors that continuously contribute to carbon stability and lability, with particular attention to the OM formation and nature, as well as the microbial activities that drive OM aggregation, degradation and eventually greenhouse gas emissions. We identified that in both aquatic and terrestrial ecosystems, microbial attributes (i.e., carbon metabolism, carbon use efficiency, necromass, enzymatic activities) play a pivotal role in transforming the carbon stock and yet they are far from being completely characterised and not often included in carbon estimations. Therefore, future research must focus on the integration of microbial components into carbon mapping and models, as well as on translating molecular-scaled studies into practical approaches. These strategies will improve carbon management and restoration across ecosystems and contribute to overcome current climate challenges.

Effects of Two Different Proportions of Microbial Formulations on Microbial Communities in Kitchen Waste Composting

The objective of this research was to investigate the effect of bulking agents on the maturity and gaseous emissions of composting kitchen waste. The composing experiments were carried out by selected core bacterial agents and universal bacterial agents for 20 days. The results demonstrated that the addition of core microbial agents effectively controlled the emission of typical odor-producing compounds. The addition of core and universal bacterial agents drastically reduced NH3 emissions by 94% and 74%, and decreased H2S emissions by 78% and 27%. The application of core microbial agents during composting elevated the peak temperature to 65 °C and in terms of efficient temperature evolution (>55 °C for 8 consecutive days). The organic matter degradation decreased by 65% from the initial values for core microbial agents were added, while for the other treatments the reduction was slight. Adding core microbial agents to kitchen waste produced mature compost with a higher germination index (GI) 112%, while other treatments did not fully mature and had a GI of <70%. Microbial analysis demonstrated that the core microbial agents in composting increased the relative abundances of Weissella, Ignatzschineria, and Bacteroides. Network and redundancy analysis (RDA) revealed that the core microbial agents enhanced the relationship between bacteria and the eight indicators (p < 0.01), thereby improving the bio transformation of compounds during composting. Overall, these results suggest that the careful selection of appropriate inoculation microorganisms is crucial for improved biological transformation and nutrient content composting efficacy of kitchen waste.

Alleviate environmental concerns with biochar as a container substrate: a review

Peat moss has desirable properties as a container substrate, however, harvesting it from peatland for greenhouse/nursery production use has disturbed peatland ecosystem and caused numerous environmental concerns. More recently, many nations have taken actions to reduce or ban peat moss production to reach the carbon neutral goal and address the environmental concerns. Also, the overuse of fertilizers and pesticides with peat moss in greenhouse/nursery production adds extra environmental and economic issues. Thus, it is urgent to find a peat moss replacement as a container substrate for greenhouse/nursery production. Biochar, a carbon-rich material with porous structure produced by the thermo-chemical decomposition of biomass in an oxygen-limited or oxygen-depleted atmosphere, has drawn researchers' attention for the past two decades. Using biochar to replace peat moss as a container substrate for greenhouse/nursery production could provide environmental and economic benefits. Biochar could be derived from various feedstocks that are regenerated faster than peat moss, and biochar possesses price advantages over peat moss when local feedstock is available. Certain types of biochar can provide nutrients, accelerate nutrient adsorption, and suppress certain pathogens, which end up with reduced fertilizer and pesticide usage and leaching. However, among the 36,474 publications on biochar, 1,457 focused on using biochar as a container substrate, and only 68 were used to replace peat moss as a container substrate component. This study provides a review for the environmental and economic concerns associated with peat moss and discussed using biochar as a peat moss alternative to alleviate these concerns.

Dissolved organic matter defines microbial communities during initial soil formation after deglaciation

Ecosystem succession and pedogenesis reshuffle the composition and turnover of dissolved organic matter (DOM) and its interactions with soil microbiome. The changes of these connections are especially intensive during initial pedogenesis, e.g. in young post-glacial areas. The temporal succession and vertical development of DOM effects on microbial community structure remains elusive. Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS), high-throughput sequencing, and molecular ecological networks, we characterized the molecular diversity of water-extractable DOM and identified its links to microbial communities in soil profiles along deglaciation chronosequence (12, 30, 40, 52, 80, and 120 years) in the southeastern Tibetan Plateau. Low-molecular-weight compound content decreased, whereas the mid- and high-molecular-weight compounds increased with succession age and soil depth. This was confirmed by the increase in double bond equivalents and averaged oxygen-to‑carbon ratios (O/C), and decrease in hydrogen-to‑carbon ratios (H/C), which reflect DOM accumulation and stabilization. Microbial community succession shifted towards the dominance of oligotrophic Acidobacteria and saprophytic Mortierellomycota, reflecting the increase of stable DOM components (H/C < 1.5 and wider O/C). Less DOM-bacterial positive networks during the succession reduced specialization of labile DOM production (such as lipid- and protein-like compounds), whereas more DOM-fungal negative networks increased specialization of stable DOM decomposition (such as tannin- and condensed aromatic-like compounds). Consequently, DOM stability is not intrinsic during initial pedogenesis: stable DOM compounds remain after fast bacterial utilization of labile DOM compounds, whereas fungi decompose slowly the remaining DOM pools.

1-Butyl-3-methylimidazolium Chloride Affects Anaerobic Digestion through Altering Organics Transformation, Cell Viability, and Microbial Community

1-Butyl-3-methylimidazolium chloride (BmimCl), an imidazolium-based ionic liquid, is considered the representative emerging persistent aquatic pollutant, and its environmental toxicity has attracted a growing concern. However, most of the investigations focused on monocultures or a single organism, with little information available on the complex syntrophic consortium that dominates the complex and successional biochemical processes, such as anaerobic digestion. In this study, the effect of BmimCl at environmentally relevant levels on glucose anaerobic digestion was therefore investigated in several laboratory-scale mesophilic anaerobic digesters to provide such support. Experimental results showed that BmimCl at 1-20 mg/L inhibited the methane production rate by 3.50-31.03%, and 20 mg/L BmimCl inhibited butyrate, hydrogen, and acetate biotransformation by 14.29%, 36.36%, and 11.57%, respectively. Toxicological mechanism studies revealed that extracellular polymeric substances (EPSs) adsorbed and accumulated BmimCl through carboxyl, amino, and hydroxyl groups, which destroyed the EPSs' conformational structure, thereby leading to the inactivation of microbial cells. MiSeq sequencing data indicated that the abundance of Clostridium_sensu_stricto_1, Bacteroides, and Methanothrix decreased by 6.01%, 7.02%, and 18.45%, respectively, in response to 20 mg/L BmimCl. Molecular ecological network analysis showed that compared with the control, the lower network complexity, fewer keystone taxa, and fewer associations among microbial taxa were found in the BmimCl-present digester, indicating the reduced stability of the microbial community.

Multi-omics eco-surveillance of bacterial community function in legacy contaminated estuary sediments

Complex legacy contamination is a major issue for many estuaries, with toxicity affecting change in bacterial communities, and their provision of associated goods and services. Sequencing surveys of bacterial community composition provide inferred function; however, additional insights may be generated by measurement of realised metabolic phenotypes. We apply multi-omics (genomics, lipidomics, and metabolomics), with traditional sediment quality analyses, to characterise sediment-associated bacterial communities in an estuary subject to legacy metal contamination (Zn, Hg, As, Cd, Cu and Pb). Analyses of bacterial composition and inferred function (genomics) are coupled with measurements of realised bacterial phenotype (metabolomics and lipidomics) at multiple industrialised and reference sites. At sites with the highest sediment metal concentrations (NTB), we also observed increased abundances of hydrocarbon and sulphuric acid metabolites, indicating additional sediment contamination. Bacterial phyla across sampled sites were dominated by Proteobacteria and Desulfobacteria. NTB sites were enriched with metabolically versatile, cooperative and biofilm forming phyla including, Zixibacteria, Spirochaetota, SAR324 clade, Proteobacteria, Latescibacterota, Desulfobacterota, Deferrisomtota and Acidobateriota; with inferred functions characterised by sulphur metabolism, pathways associated with the degradation of complex organic molecules, and fermentation. Reference sites were characterised by enhanced vitamin biosynthesis, cell wall, cofactor and carbohydrate biosynthesis, and CO₂ fixation. Measured metabolic phenotypes at NTB sites supported predicted functions, with most consistent change observed to naphthalene and aminobenzoate degradation pathways and carbohydrate metabolism (galactose, amino and nucleotide sugar). Change in NTB metabolite profiles was most highly correlated with sediment Hg concentrations, indicative of toxic exposure and potential for Hg methylation. Lipid profiles generated further insight into potential functional (hydroxy fatty acids) and community level change (ceramide phosphoethanolamines, unsaturated glycerides). Multi-omics outputs provided insights into bacterial community functions, modes of contaminant toxicity and expressed mechanisms of adaptation, necessary to better inform management decisions and predictive models in increasingly human-influenced environments.

Updated Virophage Taxonomy and Distinction from Polinton-like Viruses

Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.

Genome-Resolved Metagenomics Informs the Functional Ecology of Uncultured Acidobacteria in Redox Oscillated Sphagnum Peat

Understanding microbial niche differentiation along ecological and geochemical gradients is critical for assessing the mechanisms of ecosystem response to hydrologic variation and other aspects of global change. The lineage-specific biogeochemical roles of the widespread phylum Acidobacteria in hydrologically sensitive ecosystems, such as peatlands, are poorly understood. Here, we demonstrate that Acidobacteria sublineages in Sphagnum peat respond differentially to redox fluctuations due to variable oxygen (O₂) availability, a typical feature of hydrologic variation. Our genome-centric approach disentangles the mechanisms of niche differentiation between the Acidobacteria genera Holophaga and Terracidiphilus in response to the transient O₂ exposure of peat in laboratory incubations. Interlineage functional diversification explains the enrichment of the otherwise rare Holophaga in anoxic peat after transient O₂ exposure in comparison to Terracidiphilus dominance in continuously anoxic peat. The observed niche differentiation of the two lineages is linked to differences in their carbon degradation potential. Holophaga appear to be primarily reliant on carbohydrate oligomers and amino acids, produced during the prior period of O₂ exposure via the O₂-stimulated breakdown of peat carbon, rich in complex aromatics and carbohydrate polymers. In contrast, Terracidiphilus genomes are enriched in diverse respiratory hydrogenases and carbohydrate active enzymes, enabling the degradation of complex plant polysaccharides into monomers and oligomers for fermentation. We also present the first evidence for the potential contribution of Acidobacteria in peat nitrogen fixation. In addition to canonical molybdenum-based diazotrophy, the Acidobacteria genomes harbor vanadium and iron-only alternative nitrogenases. Together, the results better inform the different functional roles of Acidobacteria in peat biogeochemistry under global change. IMPORTANCE Acidobacteria are among the most widespread and abundant members of the soil bacterial community, yet their ecophysiology remains largely underexplored. In acidic peat systems, Acidobacteria are thought to perform key biogeochemical functions, yet the mechanistic links between the phylogenetic and metabolic diversity within this phylum and peat carbon transformations remain unclear. Here, we employ genomic comparisons of Acidobacteria subgroups enriched in laboratory incubations of peat under variable O₂ availability to disentangle the lineage-specific functional roles of these microorganisms in peat carbon transformations. Our genome-centric approach reveals that the diversification of Acidobacteria subpopulations across transient O₂ exposure is linked to differences in their carbon substrate preferences. We also identify a previously unknown functional potential for biological nitrogen fixation in these organisms. This has important implications for carbon, nitrogen, and trace metal cycling in peat systems.

Integrating Decomposers, Methane-Cycling Microbes and Ecosystem Carbon Fluxes Along a Peatland Successional Gradient in a Land Uplift Region

Peatlands are carbon dioxide (CO2) sinks that, in parallel, release methane (CH4). The peatland carbon (C) balance depends on the interplay of decomposer and CH4-cycling microbes, vegetation, and environmental conditions. These interactions are susceptible to the changes that occur along a successional gradient from vascular plant-dominated systems to Sphagnum moss-dominated systems. Changes similar to this succession are predicted to occur from climate change. Here, we investigated how microbial and plant communities are interlinked with each other and with ecosystem C cycling along a successional gradient on a boreal land uplift coast. The gradient ranged from shoreline to meadows and fens, and further to bogs. Potential microbial activity (aerobic CO2 production; CH4 production and oxidation) and biomass were greatest in the early successional meadows, although their communities of aerobic decomposers (fungi, actinobacteria), methanogens, and methanotrophs did not differ from the older fens. Instead, the functional microbial communities shifted at the fen–bog transition concurrent with a sudden decrease in C fluxes. The successional patterns of decomposer versus CH4-cycling communities diverged at the bog stage, indicating strong but distinct microbial responses to Sphagnum dominance and acidity. We highlight young meadows as dynamic sites with the greatest microbial potential for C release. These hot spots of C turnover with dense sedge cover may represent a sensitive bottleneck in succession, which is necessary for eventual long-term peat accumulation. The distinctive microbes in bogs could serve as indicators of the C sink function in restoration measures that aim to stabilize the C in the peat.

Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA

Peatland microbial community composition varies with respect to a range of biological and physicochemical variables. While the extent of peat degradation (humification) has been linked to microbial community composition along vertical stratification gradients within peatland sites, across-site variations have been relatively unexplored. In this study, we compared microbial communities across ten pristine Sphagnum-containing peatlands in the Adirondack Mountains, NY, which represented three different peat types-humic fen peat, humic bog peat, and fibric bog peat. Using 16S amplicon sequencing and network correlation analysis, we demonstrate that microbial community composition is primarily linked to peat type, and that distinct taxa networks distinguish microbial communities in each type. Shotgun metagenomic sequencing of the active water table region (mesotelm) from two Sphagnum-dominated bogs-one with fibric peat and one with humic peat-revealed differences in primary carbon degradation pathways, with the fibric peat being dominated by carbohydrate metabolism and hydrogenotrophic methanogenesis, and the humic peat being dominated by aliphatic carbon metabolism and aceticlastic methanogenesis. Our results suggest that peat humification is a major factor driving microbial community dynamics across peatland ecosystems.