Diverse Taxa Research Articles

Global diversity and biogeography of DNA viral communities in activated sludge systems

BackgroundActivated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses that regulate microbial metabolism and nutrient cycling, significantly influencing the stability of AS systems. However, our knowledge about the diversity of viral taxonomic groups and functional traits in global AS systems is still limited. To address this gap, we investigated the global diversity and biogeography of DNA viral communities in AS systems using 85,114 viral operational taxonomic units (vOTUs) recovered from 144 AS samples collected across 54 WWTPs from 13 different countries.ResultsAS viral communities and their functional traits exhibited distance-decay relationship (DDR) at the global scale and latitudinal diversity gradient (LDG) from equator to mid-latitude. Furthermore, it was observed that AS viral community and functional gene structures were largely driven by the geographic factors and wastewater types, of which the geographic factors were more important. Carrying and disseminating auxiliary metabolic genes (AMGs) associated with the degradation of polysaccharides, sulfate reduction, denitrification, and organic phosphoester hydrolysis, as well as the lysis of crucial functional microbes that govern biogeochemical cycles were two major ways by which viruses could regulate AS functions. It was worth noting that our study revealed a high abundance of antibiotic resistance genes (ARGs) in viral genomes, suggesting that viruses were key reservoirs of ARGs in AS systems.ConclusionsOur results demonstrated the highly diverse taxonomic groups and functional traits of viruses in AS systems. Viral lysis of host microbes and virus-mediated HGT can regulate the biogeochemical and nutrient cycles, thus affecting the performance of AS systems. These findings provide important insights into the viral diversity, function, and ecology in AS systems on a global scale.-K8pwvbs3fYC6bGWQ-q_MyVideo

Diversity and Convergence of Sex-Determination Mechanisms in Teleost Fish.

Sexual reproduction is prevalent across diverse taxa. However, sex-determination mechanisms are so diverse that even closely related species often differ in sex-determination systems. Teleost fish is a taxonomic group with frequent turnovers of sex-determining mechanisms and thus provides us with great opportunities to investigate the molecular and evolutionary mechanisms underlying the turnover of sex-determining systems. Here, we compile recent studies on the diversity of sex-determination mechanisms in fish. We demonstrate that genes in the TGF-β signaling pathway are frequently used for master sex-determining (MSD) genes. MSD genes arise via two main mechanisms, duplication-and-transposition and allelic mutations, with a few exceptions. We also demonstrate that temperature influences sex determination in many fish species, even those with sex chromosomes, with higher temperatures inducing differentiation into males in most cases. Finally, we review theoretical models for the turnover of sex-determining mechanisms and discuss what questions remain elusive.

A derived weedy rice × ancestral cultivar cross identifies evolutionarily relevant weediness QTLs.

Weedy rice (Oryza spp.) is a weedy relative of the cultivated rice that competes with the crop and causes significant production loss. The BHA (blackhull awned) US weedy rice group has evolved from aus cultivated rice and differs from its ancestors in several important weediness traits, including flowering time, plant height and seed shattering. Prior attempts to determine the genetic basis of weediness traits in plants using linkage mapping approaches have not often considered weed origins. However, the timing of divergence between crossed parents can affect the detection of quantitative trait loci (QTL) relevant to the evolution of weediness. Here, we used a QTL-seq approach that combines bulked segregant analysis and high-throughput whole genome resequencing to map the three important weediness traits in an F2 population derived from a cross between BHA weedy rice with an ancestral aus cultivar. We compared these QTLs with those previously detected in a cross of BHA with a more distantly related crop, indica. We identified multiple QTLs that overlapped with regions under selection during the evolution of weedy BHA rice and some candidate genes possibly underlying the evolution weediness traits in BHA. We showed that QTLs detected with ancestor-descendant crosses are more likely to be involved in the evolution of weediness traits than those detected from crosses of more diverged taxa.

Allometric-kinetic model predictions of concentration ratios for anthropogenic radionuclides across animal classes and food selection

Protection of the environment from radiation fundamentally relies on dose assessments for non-human biota. Many of these dose assessments use measured or predicted concentrations of radionuclides in soil or water combined with Concentration Ratios (CRs) to estimate whole body concentrations in animals and plants, yet there is a paucity of CR data relative to the vast number of potential taxa and radioactive contaminants in the environment and their taxon-specific ecosystems. Because there are many taxa each having very different behaviors and biology, and there are many possible bioavailable radionuclides, CRs have the potential to vary by orders-of-magnitude, as often seen in published data. Given the diversity of taxa, the International Commission on Radiological Protection (ICRP) has selected 12 non-human biota as reference animals and plants (RAPs), while the U.S. Department of Energy (DOE) uses the non-taxon specific categories of terrestrial, riparian, and aquatic animals. The question we examine here, in part, is: are these RAPs and categorizations sufficient to adequately protect all species given the broad diversity of animals in a region? To explore this question, we utilize an Allometric-Kinetic (A-K) model to calculate radionuclide-specific CRs for common animal classes, which are then further subcategorized into herbivores, omnivores, carnivores, and invertebrate detritivores. Comparisons in CRs among animal classes exhibited only small differences, but there was order of magnitude differences between herbivores, carnivores, and especially detritivores, for many radionuclides of interest. These findings suggest that the ICRP RAPs and the DOE categories are reasonable, but their accuracy could be improved by including sub-categories related to animal dietary ecology and biology. Finally, comparisons of A-K model predicted CR values to published CRs show order-of-magnitude variations, providing justification for additional studies of animal assimilation across radionuclides, environmental conditions, and animal classes.

Caregiver’s cognitive traits are associated with pup fitness in a cooperatively breeding mammal

Studies across diverse taxa have revealed the importance of early life environment and parenting on characteristics later in life. While some have shown how early life experiences can impact cognitive abilities, very few have turned this around and looked at how the cognitive skills of parents or other carers during early life affect the fitness of young. In this study, we investigate how the characteristics of carers may affect proxies of fitness of pups in the cooperatively breeding banded mongoose (Mungos mungo). We gave adult mongooses a spatial memory test and compared the results to the success of the pups those individuals cared for. Our results show a tradeoff between speed and accuracy in the spatial memory task, with those individuals which were faster to move between cups in the test arena making more erroneous re-visits to cups that they had already checked for food. Furthermore, the accuracy of their carer predicted future survival, but not weight gain of the pups and the effect was contrary to expected, with pups that were cared for by less accurate individuals being more likely to survive to adulthood. Our research also provides evidence that while younger carers were less accurate during the test, the age of the carer did not have an impact on the chance of raising young that live to sexual maturity. Our findings suggest that banded mongoose carers’ cognitive traits have fitness consequences for the young they care for, affecting the chance that these young live to maturity.

Phenotype predicts interspecific dominance hierarchies in a cloud‐forest hummingbird guild

AbstractCompetition over resources often leads to intra‐ and interspecific interactions, which can be detrimental to the individuals involved. Thus, natural selection should favor communication systems that reliably convey information regarding the relative competitive abilities of an individual, reducing the need for physically damaging confrontation. Body size, sex, age, relatedness, and ornamentation are important factors determining dominance across diverse taxa in intraspecific interactions. These traits, when perceptible, may serve as signals across species in guilds that have frequent interspecific interactions. Hummingbirds provide a tractable system to study such community dynamics due to their high frequency of interactions, variable ornamentation, diverse body sizes, fast metabolism, and large overlap in resource utilization. Even in this system, potential interactions between morphology and coloration are rarely accounted for together when analyzing dominance between species. We take a novel approach to understanding interspecific dominance by assessing behavior, morphology, and coloration across different types of behavioral interactions. Across 11 tropical montane hummingbird species, we find that dominance is predicted by wing size and some metrics of plumage coloration. However, the biological significance of these factors varies between the different dominance behaviors performed. These results inform our understanding of interspecific signaling and its role in the evolution of intraguild communication and resource competition.

Functional diversification despite structural congruence in the HipBST toxin-antitoxin system of Legionella pneumophila.

Toxin-antitoxin (TA) systems are parasitic genetic elements found in almost all bacterial genomes. They are exchanged horizontally between cells and are typically poorly conserved across closely related strains and species. Here, we report the characterization of a tripartite TA system in the bacterial pathogen Legionella pneumophila that is highly conserved across Legionella species genomes. This system (denoted HipBSTLp) is a distant homolog of the recently discovered split-HipA system in Escherichia coli (HipBSTEc). We present bioinformatic, molecular, and structural analyses of the divergence between these two systems and the functionality of this newly described TA system family. Furthermore, we provide evidence to refute previous claims that the toxin in this system (HipTLp) possesses bifunctionality as an L. pneumophila virulence protein. Overall, this work expands our understanding of the split-HipA system architecture and illustrates the potential for undiscovered biology in these abundant genetic elements.

Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits

Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.

Analysis of microbiota reveals the underlying mechanism of PHF11 in the development of Enterococcus-regulated endometriotic cysts

Endometriosis (EMS) is a prevalent disease and the etiologies has not uniform. Microbiota is associated with human diseases. To delve into the relationship between EMS and microbiota, Ectopic (EM) and eutopic (EU) endometrial tissues, pharyngeal swabs, and stools were collected from EMS patients. The microbiota composition of EM and EU partially overlapped, with similar taxon numbers and diversity, but the richness levels were significantly different. A comparison of intestinal microbes in healthy individuals (FN) and EMS patients (FE) revealed that the richness of Enterococcus, Pseudomonas, Haemophilus, and Neisseria was enhanced in FE. In addition, Enterococcus-induced mice (EFA) presented with a higher degree of lesion infiltration and a wider distribution of lesions. Proteomic analysis revealed the expression of plant homeodomain finger 11 (PHF11) was notably downregulated in EFA. And the downregulated expression of PHF11 was accompanied by the upregulated expression of interleukin 8 (IL-8). Our findings suggest a potential regulatory mechanism for PHF11 in EMS development.

Perspectives on the Grey Zone of Species Delimitation With Notes on Invertebrates in the Marine Environment

Defining species boundaries, or delimiting species, is a complex and often difficult task. Indeed, when such studies incorporate approaches that consider evolutionary mechanisms, there is much to be learned about species diversity and how the processes that play critical roles in speciation can impact species delineation. In 2021, a virtual workshop on species delimitation was held at the Smithsonian Institution National Museum of Natural History to train natural history scientists and taxonomists on the appropriate analytical tools that can be used to help delimit species when using molecular data. This perspective highlights some of the main themes discussed during that workshop while detailing three processes that can challenge any species delimitation study. Specifically, we discuss incomplete lineage sorting, gene flow, and population structure when delimiting species boundaries using molecular data. We highlight empirical studies and methodological approaches that have successfully met these challenges under various scenarios. Finally, we provide recommendations and considerations for undertaking species delimitation studies in a variety of taxa. To this end, we recommend that taxonomists fully embrace process-based species delimitation, which can provide important insights into speciation in their study systems. For those developing analytical approaches, we hope they consider incorporating less well-known taxa, such as marine invertebrates, into method testing. Marine invertebrates encompass many dark taxa across the tree of life yet represent the majority of animal phyla, many of which are vulnerable to extinction due to global ocean change. Thus, advancing species delimitation to address taxonomic revisions in these organisms will support conservation decisions on keystone ecosystems. Furthermore, the diversity of their life history strategies, the lack of obvious barriers to gene flow in the ocean environment, and their occurrence in isolated habitat patches can better inform our knowledge of speciation and the evolutionary processes that play a role in generating diversity in nature.

No evidence for direct thermal carryover effects on starvation tolerance in the obligate blood-feeder, Glossina morsitans morsitans.

Thermal stress during development can prime animals to cope better with similar conditions in later life. Alternatively, negative effects of thermal stress can persist across life stages and result in poorer quality adults (negative carryover effects). As mean temperatures increase due to climate change, evidence for such effects across diverse taxa is required. Using Glossina morsitans morsitans, a species of tsetse fly and vector of trypanosomiasis, we asked whether (i) adaptive developmental plasticity allows flies to survive for longer under food deprivation when pupal and adult temperatures are matched; or (ii) temperature stress during development persists into adulthood, resulting in a greater risk of death. We did not find any advantage of matched pupal and adult temperature in terms of improved starvation tolerance, and no direct negative carryover effects were observed. There was some evidence for indirect carryover effects-high pupal temperature produced flies of lower body mass, which, in turn, resulted in greater starvation risk. However, adult temperature had the largest impact on starvation tolerance by far: flies died 60% faster at 31°C than those experiencing 25°C, consequently reducing survival time from a median of 8 (interquartile range (IQR) 7-9) to 5 (IQR 5-5.25) days. This highlights differences in temperature sensitivity between life stages, as there was no direct effect of pupal temperature on starvation tolerance. Therefore, for some regions of sub-Saharan Africa, climate change may result in a higher mortality rate in emerging tsetse while they search for their first blood meal. This study reinforces existing evidence that responses to temperature are life stage specific and that plasticity may have limited capacity to buffer the effects of climate change.

DNA barcodes provide insights into the diversity and biogeography of the non-biting midge Polypedilum (Diptera, Chironomidae) in South America.

South America, particularly within its tropical belt, is renowned for its unparalleled high levels of species richness, surpassing other major biomes. Certain neotropical areas harbor fragmented knowledge of insect diversity and face imminent threats from biodiversity loss and climate change. Hence, there is an urgent need for rapid estimation methods to complement slower traditional taxonomic approaches. A variety of algorithms for delimiting species through single-locus DNA barcodes have been developed and applied for rapid species diversity estimates across diverse taxa. However, tree-based and distance-based methods may yield different group assignments, leading to potential overestimation or underestimation of putative species. Here, we investigate the performance of different DNA-based species delimitation approaches to rapidly estimate the diversity of Polypedilum (Chironomidae, Diptera) in South America. Additionally, we test the hypothesis that significant differences exist in the community structure of Polypedilum fauna between South America and its neighboring regions, particularly the Nearctic. Our analysis encompasses a dataset of 1492 specimens from 598 locations worldwide, with a specific focus on South America. Within this region, we analyzed a subset of 247 specimens reported from 37 locations. Using various methods including the Barcode Index Number (BIN), Bayesian Poisson tree processes (bPTP), multi-rate Poisson tree processes (mPTP), single-rate Poisson tree processes (sPTP), and generalized mixed Yule coalescent (sGMYC), we identify molecular operational taxonomic units (MOTUs) ranging from 267 to 520. Our results indicate that the sGMYC method is the most suitable for estimating putative species in our dataset, resulting in the identification of 75 species in the Neotropical region, particularly in South America. Notably, this region exhibited higher species richness in comparison to the Palearctic and Oriental realms. Additionally, our findings suggest potential differences in species composition of Polypedilum fauna between the Neotropical and the adjacent Nearctic realms, highlighting high levels of endemism and species richness in the first. These results support our hypothesis that there are substantial differences exist in species composition between the Polypedilum fauna in South America and the neighboring regions.

Ecological refugia enhance biodiversity and crop production in dryland grain production systems

Meeting global food demand while reducing biodiversity loss will require strategies that quantify and minimize conservation and production tradeoffs in agroecosystems. Ecological refugia (non-crop habitat patches) were identified in three dryland grain production systems in the Northern Great Plains and assessed for their capacity to enhance biodiversity, crop yield, and crop quality. A radial design of six 100–200 meter transects originating from the refugia and extending into crop fields was used to assess trends in plant and arthropod diversity with increasing distance from the refuge center. Plant species diversity significantly declined with distance from established refugia into crop fields in all years sampled and from a newly established refuge by the third year of data collection. Arthropod taxon diversity declined significantly with distance from refugia on two organic farms but not on a conventional farm. Fields with a refuge hosted a higher abundance of arthropods belonging to Coleoptera than fields without a refuge. Distance from refuge was the most important variable explaining grain yield and grain quality in a random forest model. Yield significantly declined with distance from refugia while grain nutritional quality, based on protein content, iron concentration, and polyphenol concentration, significantly increased with distance from refugia. Overall, ecological refugia enhanced farmland biodiversity and provided tradeoffs for marketable crop production. Moving forward, ecological refugia could serve as a multi-objective conservation practice to integrate food production and conservation goals in agroecosystems.

A novel tail: One story from the rare taxa of the coal seam microbiome

A substantial portion of global coal seam methane reserves are biogenically produced. To enhance methane production, recent research has focussed on genetic surveying of the microbial life inhabiting these coal seams. These surveys have revealed that the most abundant organisms in these microbial communities are taxa specialised in metabolism of various simple substrates, and are typically methanogens, their (presumably) syntrophic acetate-oxidising bacterial partners, and other bacterial taxa associated with biomass recycling. Although abundant, these microbes are incapable of directly accessing the vast majority of recalcitrant carbon contained within the coal geopolymer. Instead, these more abundant taxa likely rely on the low abundance but diverse taxa, known as the ‘rare taxa’, to transform the carbon within coal into simpler, more labile substrates. Since these rare taxa typically have low taxonomic resolution, their probable activities within the coal seam environment are difficult to infer using the standard 16S rDNA community surveys. Therefore, the present study aimed to develop a method for identifying and characterising these rare taxa using a metagenomic approach. Using this method, a near-complete genome from a Deltaproteobacteria sp. (CSMB_808; designation taken from the Coal Seam Microbiome reference set) was recovered from a metagenome sampling the Surat Basin, Australia, and comprised only 0.5% of the total 16S rDNA sequences recovered from this metagenome. Genetically, CSMB_808 appears to be a motile fatty acid and possibly alkane-degrader within the coal seam environment, and may play an important role in the coal-to-methane degradative pathways. Despite the near-completeness of the recovered genome, the taxonomic resolution of this deltaproteobacterium was unable to be clarified due to insufficient described close relatives. Together, the low taxonomic resolution, relatively low 16S rDNA abundance, and ability to degrade putative upstream metabolites that may facilitate methanogenesis in the coal seam environment, indicates that this method of analysis can assist in understanding other important but uncharacterised rare taxa of the coal seam microbiome. A clearer understanding of the function of these taxa would allow targeted strategies to enhance methane production, as well as contributing valuable knowledge of carbon cycling in the terrestrial subsurface.

Automated segmentation of insect anatomy from micro‐CT images using deep learning

AbstractThree‐dimensional (3D) imaging, such as microcomputed tomography (micro‐CT), is increasingly being used by organismal biologists for precise and comprehensive anatomical characterization. However, the segmentation of anatomical structures remains a bottleneck in research, often requiring tedious manual work. Here, we propose a pipeline for the fully automated segmentation of anatomical structures in micro‐CT images utilizing state‐of‐the‐art deep learning methods, selecting the ant brain as a test case. We implemented the U‐Net architecture for two‐dimensional (2D) image segmentation for our convolutional neural network (CNN), combined with pixel‐island detection. For training and validation of the network, we assembled a data set of semimanually segmented brain images of 76 ant species. The trained network predicted the brain area in ant images fast and accurately; its performance tested on validation sets showed good agreement between the prediction and the target, scoring 80% Intersection over Union (IoU) and 90% Dice Coefficient (F1) accuracy. While manual segmentation usually takes many hours for each brain, the trained network takes only a few minutes. Furthermore, our network is generalizable for segmenting the whole neural system in full‐body scans, and works in tests on distantly related and morphologically divergent insects (e.g., fruit flies). The latter suggests that methods like the one presented here generally apply across diverse taxa. Our method makes the construction of segmented maps and the morphological quantification of different species more efficient and scalable to large data sets, a step toward a big data approach to organismal anatomy.Key points Development of a deep learning‐based pipeline for the fully automated segmentation of micro‐CT images of insects, using ant brains as a starting point. Creation of an open access data set of micro‐CT images of ant heads for training and testing. Generalizable computer vision methodology, extendable across diverse taxa and anatomical features.

Broca’s area, variation and taxic diversity in early Homo from Koobi Fora (Kenya)

Because brain tissues rarely fossilize, pinpointing when and how modern human cerebral traits emerged in the hominin lineage is particularly challenging. The fragmentary nature of the fossil material, coupled with the difficulty of characterizing such a complex organ, has been the source of long-standing debates. Prominent among them are the uncertainties around the derived or primitive state of the brain organization in the earliest representatives of the genus Homo, more particularly in key regions such as the Broca’s area. By revisiting a particularly well-preserved fossil endocast from the Turkana basin (Kenya), here we confirm that early Homo in Africa had a primitive organization of the Broca’s area ca. 1.9 million years ago. Additionally, our description of KNM-ER 3732 adds further information about the variation pattern of the inferior frontal gyrus in fossil hominins, with implications for early Homo taxic diversity (i.e. one or two Homo species at Koobi Fora) and the nature of the mechanisms involved in the emergence of derived cerebral traits.

Broca's area, variation and taxic diversity in early Homo from Koobi Fora (Kenya).

Because brain tissues rarely fossilize, pinpointing when and how modern human cerebral traits emerged in the hominin lineage is particularly challenging. The fragmentary nature of the fossil material, coupled with the difficulty of characterizing such a complex organ, has been the source of long-standing debates. Prominent among them are the uncertainties around the derived or primitive state of the brain organization in the earliest representatives of the genus Homo, more particularly in key regions such as the Broca's area. By revisiting a particularly well-preserved fossil endocast from the Turkana basin (Kenya), here we confirm that early Homo in Africa had a primitive organization of the Broca's area ca. 1.9 million years ago. Additionally, our description of KNM-ER 3732 adds further information about the variation pattern of the inferior frontal gyrus in fossil hominins, with implications for early Homo taxic diversity (i.e. one or two Homo species at Koobi Fora) and the nature of the mechanisms involved in the emergence of derived cerebral traits.

Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives.

Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.

Watershed-Mediated Ecomorphological Variation: A Case Study with the Twin-Striped Clubtail Dragonfly (Hylogomphus geminatus).

Anthropogenic land-cover change is modifying ecosystems at an accelerating rate. Changes to ecomorphologically variable taxa within those ecosystems serve as early-warning signs that resources on which humans and other animals depend are being altered. One known ecomorphologically variable taxon is Hylogomphus geminatus, a species of dragonfly in the southeastern United States that shows pronounced variation in total body length across its limited geographic range. We measured total length of live as well as preserved museum specimens of H. geminatus and the sympatric species Progomphus obscurus (as a means for comparison). Both species showed significant size differences linked to HUC-8 watersheds in which they occur. H. geminatus showed additional significant differences on either side of the Apalachicola River, Florida, for all comparisons by sex. In overlapping watersheds, the species tended to show the same trends in length relative to their respective averages. Smaller body length was associated with more urban and agricultural land cover. These findings indicate that ecomorphological variation is tied to the watershed scale and point to significant variations on either side of the Apalachicola River. More thorough future analyses would be needed to verify trends in body length and identify the drivers behind them.

Methanogenesis in biogas reactors under inhibitory ammonia concentration requires community-wide tolerance

Ammonia (NH3) inhibition represents a major limitation to methane production during anaerobic digestion of organic material in biogas reactors. This process relies on co-operative metabolic interactions between diverse taxa at the community-scale. Despite this, most investigations have focused singularly on how methanogenic Archaea respond to NH3 stress. With a high-NH3 pre-adapted and un-adapted community, this study investigated responses to NH3 inhibition both at the community-scale and down to individual taxa. The pre-adapted community performed methanogenesis under inhibitory NH3 concentrations better than the un-adapted. While many functionally important phyla were shared between the two communities, only taxa from the pre-adapted community were robust to NH3. Functionally important phyla were mostly comprised of sensitive taxa (≥ 50%), yet all groups, including methanogens, also possessed tolerant individuals (10–50%) suggesting that potential mechanisms for tolerance are non-specific and widespread. Hidden Markov Model–based phylogenetic analysis of methanogens confirmed that NH3 tolerance was not restricted to specific taxonomic groups, even at the genus level. By reconstructing covarying growth patterns via network analyses, methanogenesis by the pre-adapted community was best explained by continued metabolic interactions (edges) between tolerant methanogens and other tolerant taxa (nodes). However, under non-inhibitory conditions, sensitive taxa re-emerged to dominate the pre-adapted community, suggesting that mechanisms of NH3 tolerance can be disadvantageous to fitness without selection pressure. This study demonstrates that methanogenesis under NH3 inhibition depends on broad-scale tolerance throughout the prokaryotic community. Mechanisms for tolerance seem widespread and non-specific, which has practical significance for the development of robust methanogenic biogas communities.Key points• Ammonia pre-adaptation allows for better methanogenesis under inhibitory conditions.• All functionally important prokaryote phyla have some ammonia tolerant individuals.• Methanogenesis was likely dependent on interactions between tolerant individuals.