Emission of methane by Eudrilus eugeniae and other earthworms from Brazil

Three-domain microbial communities in the gut of Pachnoda marginata larvae: A comparative study revealing opposing trends in gut compartments

This study aimed to examine the bacterial, methanogenic archaeal, and eukaryotic community structure in both the midgut and hindgut of Pachnoda marginata larvae using an amplicon sequencing approach. The goal was to investigate how various diets and the soil affect the composition of these three-domain microbial communities within the gut of insect larvae. The results indicated a notable variation in the microbial community composition among the gut compartments. The majority of the bacterial community in the hindgut was composed of Ruminococcaceae and Christensenellaceae. Nocardiaceae, Microbacteriaceae, and Lachnospiraceae were detected in midgut samples from larvae feeding on the leaf diet, whereas Sphingomonadaceae, Rhodobacteraceae, and Promicromonasporaceae dominated the bacterial community of midgut of larvae feeding on the straw diet. The diet was a significant factor that influenced the methanogenic archaeal and eukaryotic community patterns. The methanogenic communities in the two gut compartments significantly differed from each other, with the midgut communities being more similar to those in the soil. A higher diversity of methanogens was observed in the midgut samples of both diets compared to the hindgut. Overall, the microbiota of the hindgut was more host-specific, while the assembly of the midgut was more influenced by the environmental microorganisms.

Bacterial Keystone Taxa Regulate Carbon Metabolism in the Earthworm Gut

As important ecosystem engineers in soils, earthworms strongly influence carbon cycling through their burrowing and feeding activities. Earthworms do not perform these roles in isolation, because their intestines create a special habitat favorable for complex bacterial communities. However, how the ecological functioning of these earthworm-microbe interactions regulates carbon cycling remains largely unknown. To fill this knowledge gap, we investigated the bacterial community structure and carbon metabolic activities in the intestinal contents of earthworms and compared them to those of the adjacent soils in a long-term fertilization experiment. We discovered that earthworms harbored distinct bacterial communities compared to the surrounding soil under different fertilization conditions. The bacterial diversity was significantly larger in the adjacent soils than that in the earthworm gut. Three statistically identified keystone taxa in the bacterial networks, namely, Solirubrobacterales, Ktedonobacteraceae, and Jatrophihabitans, were shared across the earthworm gut and adjacent soil. Environmental factors (pH and organic matter) and keystone taxa were important determinants of the bacterial community composition in the earthworm gut. Both PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) and FAPROTAX (Functional Annotation of Prokaryotic Taxa) predicted that carbon metabolism was significantly higher in adjacent soil than in the earthworm gut, which was consistent with the average well color development obtained by the Biolog assay. Structural equation modeling combined with correlation analysis suggested that pH, organic matter, and potential keystone taxa exhibited significant relationships with carbon metabolism. This study deepens our understanding of the mechanisms underlying keystone taxa regulating carbon cycling in the earthworm gut. IMPORTANCE The intestinal microbiome of earthworms is a crucial component of the soil microbial community and nutrient cycling processes. If we could elucidate the role of this microbiome in regulating soil carbon metabolism, we would make a crucial contribution to understanding the ecological role of these gut bacterial taxa and to promoting sustainable agricultural development. However, the ecological functioning of these earthworm-microbe interactions in regulating carbon cycling has so far not been fully investigated. In this study, we revealed, first, that the bacterial groups of Solirubrobacterales, Ktedonobacteraceae, and Jatrophihabitans were core keystone taxa across the earthworm gut and adjacent soil and, second, that the environmental factors (pH and organic carbon) and keystone taxa strongly affected the bacterial community composition and exhibited close correlations with microbial carbon metabolism. Our results provide new insights into the community assembly of the earthworm gut microbiome and the ecological importance of potential keystone taxa in regulating carbon cycling dynamics.

Methanogenesis in the Digestive Tracts of the Tropical Millipedes Archispirostreptus gigas (Diplopoda, Spirostreptidae) and Epibolus pulchripes (Diplopoda, Pachybolidae)

Methanogens represent the final decomposition step in anaerobic degradation of organic matter, occurring in the digestive tracts of various invertebrates. However, factors determining their community structure and activity in distinct gut sections are still debated. In this study, we focused on the tropical millipede species Archispirostreptus gigas (Diplopoda, Spirostreptidae) and Epibolus pulchripes (Diplopoda, Pachybolidae), which release considerable amounts of methane. We aimed to characterize relationships between physicochemical parameters, methane production rates, and methanogen community structure in the two major gut sections, midgut and hindgut. Microsensor measurements revealed that both sections were strictly anoxic, with reducing conditions prevailing in both millipedes. Hydrogen concentration peaked in the anterior hindgut of E. pulchripes. In both species, the intestinal pH was significantly higher in the hindgut than in the midgut. An accumulation of acetate and formate in the gut indicated bacterial fermentation activities in the digestive tracts of both species. Phylogenetic analysis of 16S rRNA genes showed a prevalence of Methanobrevibacter spp. (Methanobacteriales), accompanied by a small fraction of so-far-unclassified "Methanomethylophilaceae" (Methanomassiliicoccales), in both species, which suggests that methanogenesis is mostly hydrogenotrophic. We conclude that anoxic conditions, negative redox potential, and bacterial production of hydrogen and formate promote gut colonization by methanogens. The higher activities of methanogens in the hindgut are explained by the higher pH of this compartment and their association with ciliates, which are restricted to this compartment and present an additional source of methanogenic substrates. IMPORTANCE Methane (CH₄) is the second most important atmospheric greenhouse gas after CO₂ and is believed to account for 17% of global warming. Methanogens are a diverse group of archaea and can be found in various anoxic habitats, including digestive tracts of plant-feeding animals. Termites, cockroaches, the larvae of scarab beetles, and millipedes are the only arthropods known to host methanogens and emit large amounts of methane. Millipedes are ranked as the third most important detritivores after termites and earthworms, and they are considered keystone species in many terrestrial ecosystems. Both methane-producing and non-methane-emitting species of millipedes have been observed, but what limits their methanogenic potential is not known. In the present study, we show that physicochemical gut conditions and the distribution of symbiotic ciliates are important factors determining CH₄ emission in millipedes. We also found close similarities to other methane-emitting arthropods, which might be associated with their similar plant-feeding habits.

Ecological role of earthworm intestinal bacteria in terrestrial environments: A review

Increasing evidence demonstrated the critical role the earthworm gut played in sustaining earthworm's metabolism and transformation of nutrients and pollutants in the environment. Being rich in nutrients, the earthworm gut is favorable for the colonization of (facultative) anaerobic bacteria, which bridge the host earthworm gut with adjacent terrestrial environment. Therefore, the status quo of earthworm gut research was primarily reviewed in this work. It was found that most studies focused on the bacterial composition and diversity of the earthworm gut, and their potential application in nutrient element and pollutant transformation, such as nitrification, methanogens, heavy metal detoxification, etc. Yet limited information was available about the specific mechanism of intestinal bacteria in nutrient and pollutant transformation. Therefore, in this work we highlighted the current problems and concluded the future prospect of worm's intestinal bacteria research. On one hand, high throughput sequencing and bioinformatics tools are critical to break the bottleneck in the intestinal bacteria research via clarifying the molecular mechanism involved in the transformation processes described above. In addition, a global dataset concerning worm gut bacteria will be needed to provide comprehensive information about intestinal bacteria pool, and act as a communication platform to further encourage the progress of worm gut research.

Earthworms offset straw-induced increase of greenhouse gas emission in upland rice production

Increasing water scarcity and rapid socio-economic development are driving farmers in Asia to transform traditionally flooded rice cropping systems into non-flooded crop production. The management of earthworms in non-flooded rice fields appears to be a promising strategy to support residue recycling and mitigate greenhouse gas (GHG) emissions triggered by residue amendment. We conducted a field experiment on non-flooded rainfed rice fields, with and without residue amendment. In-situ mesocosms were inoculated with endogeic earthworms (Metaphire sp.), with either low (ET1: 150 individuals m^-2), or high density (ET2: 450 individuals m^-2), and a control (ET0: no earthworms). We measured GHG emissions (methane (CH₄); nitrous oxide (N₂O); carbon dioxide (CO₂)) twice a week during the cropping season with static chambers. Effects of earthworms on yield and root growth were additionally assessed. Earthworms offset the enormous increase of CH₄ emissions induced by straw amendment (from 4.6 ± 5 to 75.3 ± 46 kg CH₄-C ha^-1 in ET0). Earthworm activity significantly reduced CH₄ release, particularly at ET2, by more than one-third (to 22 ± 15 kg CH₄-C ha^-1). In contrast, earthworm inoculation did not affect N₂O emission. Straw amendment more than doubled the global warming potential (GWP). Earthworms reduced GWP by 39% at low (ET1) and 55% at high densities (ET2). Earthworm activity reduced root mass density under conditions of straw amendment but did not affect yield. Earthworms can significantly reduce detrimental effects of rice crop residue amendment on GHG release under upland rice production. Organic carbon (C) might be preserved in earthworm casts and thereby limit C availability for CH₄ production. At the same time, earthworm activity might increase methanotrophic CH₄ consumption, due to improved soil aeration or less root exudates. Consequently, earthworms have a strong potential for regulating ecosystem functions related to rice straw decomposition, nutrient allocation and thus GHG reduction.

Temporal Variation of Earthworm Impacts on Soil Organic Carbon under Different Tillage Systems

Previous research has shown the varied effect of earthworms on soil carbon dynamics. We carried out a 180-day incubation experiment with earthworms and maize residue additions under conventional tillage (CT) and no tillage (NT) system conditions to quantify the earthworm effect in the black soil of northeastern China. Earthworms did not affect soil CO₂ emissions, while residue addition significantly increased such emissions. The effects of earthworms on dissolved organic carbon (DOC) and microbial biomass carbon (MBC) gradually weakened with time in CT with and without residue addition, but gradually increased with time in NT with residue addition. In the CT system, earthworms accelerated the soil organic carbon (SOC) mineralization; and the newly added residue decomposed into SOC. In the NT system, earthworms accelerated the decomposition of native residues increasing the SOC content; this increase in decomposition rates by earthworms was greater than the inhibitory effect imposed by the addition of the new residue. Earthworms and residues combine to play a single role in CT and NT. This result will help in the understanding of the role of earthworms and residue in SOC dynamics, and in the development of management strategies to improve SOC.

Mobile Incubator for Iron(III) Reduction in the Gut of the Soil-Feeding Earthworm Pheretima guillelmi and Interaction with Denitrification

Diets of soil-feeding earthworms contain abundant nitrate and iron(III) oxides, which are potential electron acceptors for mineralization of organic compounds. The earthworm gut provides an ideal habitat for ingested iron(III)-reducing microorganisms. However, little is known about iron(III) reduction and its interaction with other processes in the guts of earthworms. Here, we determined the dynamics of iron(III) and revealed its interaction with the turnover of organic acids and nitrate in the gut of the earthworm Pheretima guillelmi. Samples from gut contents combined with anoxic incubation were used for chemical analysis and 16S rRNA based Illumina sequencing. Chemical analysis showed that higher ratios of iron(II)/iron(III), nitrite/nitrate, and more abundant organic acids were contained in the in vivo gut of the earthworm P. guillelmi than those in the in situ soil. A higher rate of iron(III) reduction was detected in treatments of microcosmic incubation with gut contents (IG gut) than that with soil (IG soil), and nitrate reduction occurred earlier than iron(III) reduction in both treatments. Potential iron(III) reducers were dominated by fermentative genera Clostridium, Bacillus, and Desulfotomaculum in the treatment of IG gut, while they were dominated by dissimilatory iron(III)-reducing genera Geobacter in the treatment of IG soil. The iron(III)-reducing microbial community shared several genera with denitrifers in the treatment of IG gut, revealing a close link between iron(III) reduction and denitrification in the gut of earthworms. Collectively, our findings demonstrated that iron(III) reduction occurred along the gut and provided novel insights into the great contribution of earthworm gut microbiota on Fe and the associated C and N cycling in soil environments.

Protein- and RNA-Enhanced Fermentation by Gut Microbiota of the Earthworm Lumbricus terrestris

Earthworms are a dominant macrofauna in soil ecosystems and have determinative effects on soil fertility and plant growth. These invertebrates feed on ingested material, and gizzard-linked disruption of ingested fungal and bacterial cells is conceived to provide diverse biopolymers in the anoxic alimentary canals of earthworms. Fermentation in the gut is likely important to the utilization of ingested biopolymer-derived compounds by the earthworm. This study therefore examined the fermentative responses of gut content-associated microbes of the model earthworm Lumbricus terrestris to (i) microbial cell lysate (to simulate gizzard-disrupted cells) and (ii) dominant biopolymers of such biomass, protein, and RNA. The microbial cell lysate augmented the production of H₂, CO₂, and diverse fatty acids (e.g., formate, acetate, propionate, succinate, and butyrate) in anoxic gut content microcosms, indicating that the cell lysate triggered diverse fermentations. Protein and RNA also augmented diverse fermentations in anoxic microcosms of gut contents, each yielding a distinct product profile (e.g., RNA yielded H₂ and succinate, whereas protein did not). The combined product profile of protein and RNA treatments was similar to that of cell lysate treatments, and 16S rRNA-based analyses indicated that many taxa that responded to cell lysate were similar to taxa that responded to protein or RNA. In particular, protein stimulated Peptostreptococcaceae, Clostridiaceae, and Fusobacteriaceae, whereas RNA stimulated Aeromonadaceae. These findings demonstrate the capacity of gut-associated obligate anaerobes and facultative aerobes to catalyze biopolymer-driven fermentations and highlight the potential importance of protein and RNA as substrates linked to the overall turnover dynamics of organic carbon in the alimentary canal of the earthworm.

IMPORTANCE The subsurface lifestyle of earthworms makes them an unnoticed component of the terrestrial biosphere. However, the propensity of these invertebrates to consume their home, i.e., soil and litter, has long-term impacts on soil fertility, plant growth, and the cycling of elements. The alimentary canals of earthworms can contain up to 500 ml anoxic gut content per square meter of soil, and ingested soil may contain 10⁹ or more microbial cells per gram dry weight, considerations that illustrate that enormous numbers of soil microbes are subject to anoxia during gut passage. Feeding introduces diverse sources of biopolymers to the gut, and the gut fermentation of biopolymers could be important to the transformation of matter by the earthworm and its capacity to utilize fermentation-derived fatty acids. Thus, this study examined the capacity of microbes in earthworm gut contents to ferment protein and RNA, dominant biopolymers of cells that become disrupted during gut passage.

Differential Engagement of Fermentative Taxa in Gut Contents of the Earthworm Lumbricus terrestris

The earthworm gut is an anoxic, saccharide-rich microzone in aerated soils. The apparent degradation of diverse saccharides in the alimentary canal of the model earthworm Lumbricusterrestris is concomitant with the production of diverse organic acids, indicating that fermentation is an ongoing process in the earthworm gut. However, little is known about how different gut-associated saccharides are fermented. The hypothesis of this investigation was that different gut-associated saccharides differentially stimulate fermentative microorganisms in gut contents of L. terrestris This hypothesis was addressed by (i) assessing the fermentation profiles of anoxic gut content microcosms that were supplemented with gut-associated saccharides and (ii) the concomitant phylogenic analysis of 16S rRNA sequences. Galactose, glucose, maltose, mannose, arabinose, fucose, rhamnose, and xylose stimulated the production of fermentation products, including H2, CO2, acetate, lactate, propionate, formate, succinate, and ethanol. Fermentation profiles were dependent on the supplemental saccharide (e.g., glucose yielded large amounts of H2 and ethanol, whereas fucose did not, and maltose yielded large amounts of lactate, whereas mannose did not). Approximately 1,750,000 16S rRNA sequences were affiliated with 37 families, and phylogenic analyses indicated that a respective saccharide stimulated a subset of the diverse phylotypes. An Aeromonas-related phylotype displayed a high relative abundance in all treatments, whereas key Enterobacteriaceae-affiliated phylotypes were stimulated by some but not all saccharides. Collectively, these results reinforce the likelihood that (i) different saccharides stimulate different fermentations in gut contents of the earthworm and (ii) facultative aerobes related to Aeromonadaceae and Enterobacteriaceae can be important drivers of these fermentations.IMPORTANCE The feeding habits of earthworms influence the turnover of elements in the terrestrial biosphere. The alimentary tract of the earthworm constitutes an anoxic saccharide-rich microzone in aerated soils that offers ingested microbes a unique opportunity for anaerobic growth. The fermentative activity of microbes in the alimentary tract are responsible for the in situ production of (i) organic compounds that can be assimilated by the earthworm and (ii) H2 that is subject to in vivo emission by the earthworm and can be trophically linked to secondary microbial events in soils. To gain insight on how fermentative members of the gut microbiome might respond to the saccharide-rich alimentary canal, this study examines the impact of diverse gut-associated saccharides on the differential activation of fermentative microbes in gut contents of the model earthworm L. terrestris.

Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil

The anoxic saccharide-rich conditions of the earthworm gut provide an ideal transient habitat for ingested microbes capable of anaerobiosis. It was recently discovered that the earthworm Eudrilus eugeniae from Brazil can emit methane (CH4) and that ingested methanogens might be associated with this emission. The objective of this study was to resolve trophic interactions of bacteria and methanogens in the methanogenic food web in the gut contents of E. eugeniae. RNA-based stable isotope probing of bacterial 16S rRNA as well as mcrA and mrtA (the alpha subunit of methyl-CoM reductase and its isoenzyme, respectively) of methanogens was performed with [(13)C]-glucose as a model saccharide in the gut contents. Concomitant fermentations were augmented by the rapid consumption of glucose, yielding numerous products, including molecular hydrogen (H2), carbon dioxide (CO2), formate, acetate, ethanol, lactate, succinate and propionate. Aeromonadaceae-affiliated facultative aerobes, and obligate anaerobes affiliated to Lachnospiraceae, Veillonellaceae and Ruminococcaceae were associated with the diverse fermentations. Methanogenesis was ongoing during incubations, and (13)C-labeling of CH4 verified that supplemental [(13)C]-glucose derived carbon was dissimilated to CH4. Hydrogenotrophic methanogens affiliated with Methanobacteriaceae and Methanoregulaceae were linked to methanogenesis, and acetogens related to Peptostreptoccocaceae were likewise found to be participants in the methanogenic food web. H2 rather than acetate stimulated methanogenesis in the methanogenic gut content enrichments, and acetogens appeared to dissimilate supplemental H2 to acetate in methanogenic enrichments. These findings provide insight on the processes and associated taxa potentially linked to methanogenesis and the turnover of organic carbon in the alimentary canal of methane-emitting E. eugeniae.

Anaerobic trophic interactions of contrasting methane-emitting mire soils: processes versus taxa

Natural wetlands such as mires contribute up to 33% to the global emission of methane. The emission of methane is driven by trophic interactions of anaerobes that collectively degrade biopolymers. The hypothesis of this study was that these interactions in contrasting methane-emitting mire soils are functionally similar but linked to dissimilar taxa. This hypothesis was addressed by evaluating anaerobic processes and microbial taxa of eutrophic, mesotrophic and oligotrophic mire soils. Glucose was fermented to various products (e.g. H2, CO2, butyrate, acetate). Acetoclastic methanogenesis occurred, and acetogenesis and methanogenesis transformed H2-CO2 to acetate and methane, respectively. Although product profiles, cultivable cell numbers and gene copy numbers [mcrA (encodes alpha-subunit of methyl-CoM reductase) and 16S rRNA genes] were similar for all mire soils, only approximately 15% of detected family-level bacteria and species-level methanogens were shared by all mire soils. Approximately, 40% of the detected family-level taxa of each mire soil have no cultured isolates. Acidic conditions appeared to restrict the number of dominant phylotypes. The results indicated (a) that microbial processes which drive methanogenesis are similar but facilitated by dissimilar microbial communities in contrasting mire soils and (b) that mire soils harbor a large number of taxa with no cultured isolates.

The effect of anthropogenic arsenic contamination on the earthworm microbiome

Earthworms are globally distributed and perform essential roles for soil health and microbial structure. We have investigated the effect of an anthropogenic contamination gradient on the bacterial community of the keystone ecological species Lumbricus rubellus through utilizing 16S rRNA pyrosequencing for the first time to establish the microbiome of the host and surrounding soil. The earthworm-associated microbiome differs from the surrounding environment which appears to be a result of both filtering and stimulation likely linked to the altered environment associated with the gut micro-habitat (neutral pH, anoxia and increased carbon substrates). We identified a core earthworm community comprising Proteobacteria (∼50%) and Actinobacteria (∼30%), with lower abundances of Bacteroidetes (∼6%) and Acidobacteria (∼3%). In addition to the known earthworm symbiont (Verminephrobacter sp.), we identified a potential host-associated Gammaproteobacteria species (Serratia sp.) that was absent from soil yet observed in most earthworms. Although a distinct bacterial community defines these earthworms, clear family- and species-level modification were observed along an arsenic and iron contamination gradient. Several taxa observed in uncontaminated control microbiomes are suppressed by metal/metalloid field exposure, including eradication of the hereto ubiquitously associated Verminephrobacter symbiont, which raises implications to its functional role in the earthworm microbiome.