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Identification Of Animal Behavioral Strategy By Inverse Reinforcement Learning ~ Its Application To Thermotaxis In C. elegans ~

Animals are able to reach a desired state in an environment by controlling various behavioral patterns. Identification of the behavioral strategy used for this control is important for understanding animals decision-making and is fundamental to dissect information processing done by the nervous system. However, methods for quantifying such behavioral strategies have not been fully established. In this study, we developed an inverse reinforcement-learning (IRL) framework to identify an animals behavioral strategy from behavioral time-series data. As a particular target, we applied this framework to C. elegans thermotactic behavior; after cultivation at a constant temperature with or without food, the fed and starved worms prefer and avoid from the cultivation temperature on a thermal gradient, respectively. Our IRL approach revealed that the fed worms used both absolute and temporal derivative of temperature and that their strategy comprised mixture of two strategies: directed migration (DM) and isothermal migration (IM). The DM is a strategy that the worms efficiently reach to specific temperature, which explained thermotactic behaviors of the fed worms. The IM is a strategy that the worms track along a constant temperature, which reflects isothermal tracking well observed in previous studies. We also showed the neural basis underlying the strategies, by applying our method to thermosensory neuron-deficient worms. In contrast to fed animals, the strategy of starved animals indicated that they escaped the cultivation temperature using only absolute, but not temporal derivative of temperature. Thus, our IRL-based approach is capable of identifying animal strategies from behavioral time-series data and will be applicable to wide range of behavioral studies, including decision-making of other organisms.\n\nAuthor SummaryUnderstanding animal decision-making has been a fundamental problem in neuroscience and behavioral ecology. Many studies analyze actions that represent decision-making in behavioral tasks, in which rewards are artificially designed with specific objectives. However, it is impossible to extend this artificially designed experiment to a natural environment, because in a natural environment, the rewards for freely-behaving animals cannot be clearly defined. To this end, we must reverse the current paradigm so that rewards are identified from behavioral data. Here, we propose a new reverse-engineering approach (inverse reinforcement learning) that can estimate a behavioral strategy from time-series data of freely-behaving animals. By applying this technique with thermotaxis in C. elegans, we successfully identified the reward-based behavioral strategy.

neuroscience

Assessing species biomass contributions in microbial communities via metaproteomics

Assessment of microbial community composition is the cornerstone of microbial ecology. Microbial community composition can be analyzed by quantifying cell numbers or by quantifying biomass for individual populations. However, as cell volumes can differ by orders of magnitude, these two approaches yield vastly different results. Methods for quantifying cell numbers are already available (e.g. fluorescence in situ hybridization, 16S rRNA gene amplicon sequencing), yet methods for assessing community composition in terms of biomass are lacking.\n\nWe developed metaproteomics based methods for assessing microbial community composition using protein abundance as a measure for biomass contributions of individual populations. We optimized the accuracy and sensitivity of the method using artificially assembled microbial communities and found that it is less prone to some of the biases found in sequencing-based methods. We applied the method using communities from two different environments, microbial mats from two alkaline soda lakes and saliva from multiple individuals.

microbiology

High-resolution single-cell sequencing of malaria parasites

Single-cell genomics is a powerful tool for determining the genetic structure of complex communities of unicellular organisms. Patients infected with the malaria-causing parasite, Plasmodium falciparum, often carry multiple, genetically distinct parasites. Little is known about the diversity and relatedness of these lineages. We have developed an improved single-cell genomics protocol to reconstruct individual haplotypes from infections, a necessary step in uncovering parasite ecology within the host. This approach captures singly-infected red blood cells (iRBCs) by fluorescence-activated cell sorting (FACS) prior to whole genome amplification (WGA) and whole genome sequencing (WGS). Here, we demonstrate that parasites in late cell cycle stages, which contain increased DNA content, are far superior templates for generating high quality genomic data. Targeting of these cells routinely generates near-complete capture of the 23Mb P. falciparum genome (mean breadth of coverage 90.7%) at high efficiency. We used this approach to analyze the genomes of 48 individual cells from a polyclonal malaria infection sampled in Chikhwawa, Malawi. This comprehensive dataset enabled high-resolution estimation of the clonality and the relatedness of parasite haplotypes within the infection, long-standing problems in malaria biology.

genomics

Consistent Individual Differences Drive Collective Behaviour And Group Functioning Of Schooling Fish

The ubiquity of consistent inter-individual differences in behaviour ( animal personalities) 1,2, suggests they may constitute a fundamental component of animal groups that may drive their functioning 3,4. Despite increasing evidence that highlights their importance 5-16, we still lack a unified mechanistic frame-work to explain and predict how inter-individual differences may affect collective behaviour. Here we investigate how differences in individual behavioural tendencies affect the group structure, movement dynamics, and foraging behaviour of animal groups using free-swimming stickleback fish (Gasterosteus aculeatus). Analysis of high-resolution tracking data of known individuals demonstrates that, across a range of contexts, consistent inter-individual differences in social proximity were strongly linked to speed and, together with boldness predicted spatial positioning and leadership within groups, differences in structure and movement dynamics between groups, as well as individual and group foraging performance. These effects of inter-individual behavioural variation on group-level states emerged naturally from a generic model of heterogeneous, self-organising groups. Our study combines experimental and theoretical evidence for a simple mechanism to explain variation in the emergence of structure, dynamics, and functional capabilities of groups across social and ecological scales. In addition, we show that individual performance was conditional to the group composition, providing a potential basis for social selection driving behavioural differentiation between individuals.

animal behavior and cognition

Are Global Hotspots Of Endemic Richness Shaped By Plate Tectonics?

Singular regions of the globe harbour a disproportionally large fraction of extant biodiversity. Spatial biodiversity gradients are frequently associated to extant ecological conditions using statistical models, but more rarely to paleo-environmental conditions, especially beyond the Quaternary. On one hand the role of plate tectonics in shaping the extant diversity of lineages is supported by numerous phylogenetic and fossil evidences, and on the other hand the spatial variation of biodiversity across the globe is rarely associated to geodynamic variables. In this study, we propose that plate tectonics explain the current location of hotspots of endemic richness across the globe. As an illustration, we used paleogeographies in a model, which quantifies through time and for each cell the potential dispersal across disconnected habitat patches. Rare events of dispersal across dynamic straits of unsuitable habitats allows species colonisation and that a subsequent absence of gene flow could lead to in-situ speciation. We evaluated whether this process could pinpoint the locations of hotspots of endemic richness computed from the ranges of 181,603 species across 14 taxonomic groups. The significant congruence between the regions highlighted by the model and the endemic richness provides evidences of the contribution of plate tectonics in shaping global biodiversity gradients. Places with high tectonic complexity, predominantly located at the confluence of major lithospheric plates such as the Mediterranean basin, Central America, Madagascar and South East Asia likely provided favourable circumstances for allopatric speciation and the emergence of new species across straits. While our illustration supports the role of plate tectonics, accounting for deep time geological events in spatial models of extant biodiversity is not straightforward. Future research should develop quantitative spatial models of biodiversity including the dynamic of ancient habitats.

evolutionary biology

The threshold of binocularity: natural image statistics explain the reduction of visual acuity in peripheral vision.

Visual acuity is greatest in the centre of the visual field, peaking in the fovea and degrading significantly towards the periphery. The rate of decay of visual performance with eccentricity depends strongly on the stimuli and task used in measurement. While detailed measures of this decay have been made across a broad range of tasks, a comprehensive theoretical account of this phenomenon is lacking. We demonstrate that the decay in visual performance can be attributed to the efficient encoding of binocular information in natural scenes. The efficient coding hypothesis holds that the early stages of visual processing attempt to form an efficient coding of ecologically valid stimuli. Using Independent Component Analysis to learn an efficient coding of stereoscopic images, we show that the ratio of binocular to monocular components varied with eccentricity at the same rate as human stereo acuity and Vernier acuity. Our results demonstrate that the organisation of the visual cortex is dependent on the underlying statistics of binocular scenes and, strikingly, that monocular acuity depends on the mechanisms by which the visual cortex processes binocular information. This result has important theoretical implications for understanding the encoding of visual information in the brain.

neuroscience

Relic DNA contributes minimally to estimates of microbial diversity

Extracellular or \"relic\" DNA is one of the largest pools of nucleic acids in the mbiosphere 1,2. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also bias estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SAD) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33 % of the total bacterial DNA pool, but exceeded 80 % in some samples. Despite its abundance, relic DNA had no effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Rather, our findings are consistent with the expectation that relic DNA sequences degrade in proportion to their abundance and therefore may contribute minimally to estimates of microbial diversity.

microbiology

A persistent lack of International representation on editorial boards in biology

The scholars comprising journal editorial boards play a critical role in defining the trajectory of knowledge in their field. Nevertheless, studies of editorial board composition remain rare, especially those focusing on journals publishing research in the increasingly globalized fields of science, technology, engineering, and math (STEM). Using metrics for quantifying the diversity of ecological communities, we quantified international representation on the 1985-2014 editorial boards of twenty-four environmental biology journals. Over the course of three decades there were 3831 unique scientists based in 70 countries that served as editors. The size of the editorial community increased over time - there were 420% more editors serving in 2014 than in 1985 - as did the number of countries in which editors were based. Nevertheless, editors based outside the Global North (the group of economically developed countries with high per capita Gross Domestic Product (GDP) that collectively concentrate most global wealth) were extremely rare. Furthermore, 67.06% of all editors were based in either the USA or UK. Consequently, Geographic Diversity - already low in 1985 - remained unchanged through 2014. We argue that this limited geographic diversity can detrimentally affect the creativity of scholarship published in journals, the progress and direction of research, the composition of the STEM workforce, and the development of science in Latin America, Africa, the Middle East, and much of Asia (i.e., the Global South).

scientific communication and education

Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp

Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present the MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures. It accepts single-end or paired-end sequences in fasta or fastq format from various sequencing platforms. It includes read quality control, and merging of forward and reverse reads of paired-end reads. It makes use of UPARSE, Mothur, and the SILVA database for clustering, removal of chimeric reads, taxonomic classification and generation of diversity metrics. The pipeline has been validated with a mock community of known composition. MetaAmp provides a convenient web interface as well as command line interface. It is freely available at: http://ebg.ucalgary.ca/metaamp. Since its launch two years ago, MetaAmp has been used >2,800 times, by many users worldwide.

bioinformatics

Bistability In Fluorescence From A Purple Non-Sulfur Bacteria

Bistable optical emission has been observed for photosynthetic purple non-sulfur bacteria Rhodobacter capsulatus SB1003. The microbes respond to UV excitation (at 395nm) in a bifurcating way one branch corresponding to increase and the other corresponding to diminishing fluorescent emission in the range 590-685nm.The switching between such bifurcating branches can be observed when parameters like concentration, temperature are varied or static magnetic field is applied. Thus switching from amplification to reduction occurs if fluorophore concentration lowered. Again if temperature is lowered a steady quenching (instead of amplification) of fluorescence is observed. However presence of magnetic field of the order of 0.5 T reverts this and once again the systems resumes its fluoresence amplifying state. We propose that aggregation of bacterial porphyrin and regulation of such aggregation by photon excitation may explain this bistablity. Possible ecological implication of the photosynthetic bistability is suggested.

systems biology

The Genomic Landscape Of Tree Rot In Phellinus noxius And Its Hymenochaetales Members

The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomics analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood-decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens, and trunk pathogen Porodaedalea pini. Many gene families of lignin-degrading enzymes were identified from these fungi, reflecting their ability as white rot fungi. Comparing against distant fungi highlighted the expansion of 1,3-beta-glucan synthases in P. noxius, which may account for its fast-growing attribute. We identified 13 linkage groups conserved within Agaricomycetes, suggesting the evolution of stable karyotypes. We determined that P. noxius has a bipolar heterothallic mating system, with unusual highly expanded ~60 kb A locus as a result of accumulating gene transposition. We investigated the population genomics of 60 P. noxius isolates across multiple islands of the Asia Pacific region. Whole-genome sequencing showed this multinucleate species contains abundant poly-allelic single-nucleotide-polymorphisms (SNPs) with atypical allele frequencies. Different patterns of intra-isolate polymorphism reflect mono-/heterokaryotic states which are both prevalent in nature. We have shown two genetically separated lineages with one spanning across many islands despite the geographical barriers. Both populations possess extraordinary genetic diversity and show contrasting evolutionary scenarios. These results provide a framework to further investigate the genetic basis underlying the fitness and virulence of white rot fungi.

genomics

Exon-Based Phylogenomics Strengthens The Phylogeny Of Neotropical Cichlids And Identifies Remaining Conflicting Clades (Cichlomorphae: Cichlidae: Cichlinae)

The phenotypic, geographic, and species diversity of cichlid fishes have made them a group of great interest for studying evolutionary processes. Here we present a targeted-exon next-generation sequencing approach for investigating the evolutionary relationships of cichlid fishes (Cichlidae), with focus on the Neotropical subfamily Cichlinae using a set of 923 primarily single-copy exons designed through mining of the Nile tilapia (Oreochromis niloticus) genome. Sequence capture and assembly were robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that consisted of 128 Neotropical species, six African taxa, and five Indo-Malagasy cichlids. Gene and species trees were calculated using alternative partitioning schemes and reconstruction methods. In general, all methods yielded similar topologies to previously hypothesized relationships within the Cichlinae and clarified several relationships that were previously poorly supported or in conflict. Additional work will be needed to fully resolve all aspects of Cichlinae phylogeny. Overall, this approach yielded a well-resolved phylogeny of Neotropical cichlids that will be of utility for future assessments of the evolutionary and ecological processes within this diverse group of fishes. Furthermore, the general methodology employed here of exon targeting and capture should be applicable to any group of organisms with the availability of a reference genome.

evolutionary biology

Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics

The evolution of the suite of morphological and behavioral adaptations underlying the ecological success of army ants has been the subject of considerable debate. This \"army ant syn-drome\" has been argued to have arisen once or multiple times within the ant subfamily Dorylinae. To address this question I generated data from 2,166 loci and a comprehensive taxon sampling for a phylogenetic investigation. Most analyses show strong support for convergent evolution of the army ant syndrome in the Old and New World but certain relationships are sensitive to analytics. I examine the signal present in this data set and find that conflict is diminished when only loci less likely to violate common phylogenetic model assumptions are considered. I also provide a temporal and spatial context for doryline evolution with timecalibrated, biogeographic, and diversification rate shift analyses. This study underscores the need for cautious analysis of phylogenomic data and calls for more efficient algorithms employing better-fitting models of molecular evolution.\n\nSignificanceRecent interpretation of army ant evolution holds that army ant behavior and morphology originated only once within the subfamily Dorylinae. An inspection of phylogenetic signal in a large new data set shows that support for this hypothesis may be driven by bias present in the data. Convergent evolution of the army ant syndrome is consistently supported when sequences violating assumptions of a commonly used model of sequence evolution are excluded from the analysis. This hypothesis also fits with a simple scenario of doryline biogeography. These results highlight the importance of careful evaluation of signal and conflict within phylogenomic data sets, even when taxon sampling is comprehensive.

evolutionary biology

Fast Periodic Stimulation (FPS): A Highly Effective Approach In fMRI Brain Mapping

Functional magnetic resonance imaging (fMRI) is a major technique for human brain mapping. We present a Fast Periodic Stimulation (FPS) fMRI approach, demonstrating its high effectiveness in defining category-selective brain regions. Observers see a dynamic stream of widely variable natural object images alternating at a fast rate (6 images/sec). Every 9 seconds, a short burst of variable face images contrasting with objects in pairs induces an objective 0.111 Hz face-selective neural response in the ventral occipito-temporal cortex and beyond. A model-free Fourier analysis achieves a two-fold increase in signal-to-noise ratio compared to a conventional block-design approach with identical stimuli. Periodicity of category contrast and random variability among images minimize low-level visual confounds while preserving naturalness of the stimuli, leading to the highest values (80-90%) of test-retest reliability yet reported in this area of research. FPS-fMRI opens a new avenue for understanding brain function with low temporal resolution methods.\n\nHighlightsFPS-fMRI achieves a two-fold increase in peak SNR over conventional approach\n\nFPS-fMRI reveals comprehensive extended face-selective areas including ATL\n\nFPS-fMRI achieves high specificity by minimizing influence of low-level visual cues\n\nFPS-fMRI achieves very high test-retest reliability (80%-90%) in spatial activation map\n\neTOC BlurbIn Brief\n\nGao et al. present a novel FPS-fMRI approach, which achieves a two-fold increase in peak signal-to-noise ratio in defining the neural basis of visual categorization while preserving ecological validity, minimizing low-level visual confounds and reaching very high (80%-90%) test-retest reliability.

neuroscience

Extensive Sexual Wing Shape Dimorphism In Drosophila melanogaster, Ceratitis capitata, And Musca domestica

The ability of powered flight in insects facilitated their great evolutionary success allowing them to occupy various ecological niches. Beyond this primary task, wings are often involved in various premating behaviors, such as the generation of courtship songs and the initiation of mating in flight. These specific functions imply special adaptations of wing morphology, as well as sex-specific wing morphologies. Although wing morphology has been extensively studied in Drosophila melanogaster, a comprehensive understa nding of sexual wing shape dimorphisms and developmental plasticity is missing for other Diptera. Therefore, we raised flies of the three Diptera species Drosophila melanogaster, Ceratitis capitata and Musca domestica at different environmental conditions and applied geometric morphometrics to analyze wing shape. Our data showed extensive interspecific differences in wing shape, as well as a clear sexual wing shape dimorphism in all three species. We revealed an impact of different rearing temperatures wing shape in all three species, which was mostly explained by plasticity in wing size in D. melanogaster. Rearing densities had significant effects on allometric wing shape in D. melanogaster, while no obvious effects were observed for the other two species. Additionally, we do not find evidence for sex-specific response to different rearing conditions in all three species. We determined species-specific and common trends in shape alterations, and we hypothesize developmental and functional implications of our data. Contribution to the Field StatementThe size and shape of organisms and organs must be tightly controlled during development to ensure proper functionality. However, morphological traits vary considerably in nature contributing to phenotypic diversity. Such variation can be the result of evolutionary adaptations as well as plasticity for example as reaction to changing environmental conditions during development. It is therefore a major aim in Biology to unravel the processes that control differences in adult morphology. Insect wings are excellent models to study how organ size and shape evolves because they facilitate basic tasks such as mating and feeding. Accordingly, a tremendous variety of wings sizes and shapes evolved in nature. Additionally, plasticity in wing morphology in response to different rearing conditions has been observed in many insects contributing to phenotypic diversity. In this work we applied Geometric Morphometrics to study wing shape in the three Diptera species: the Mediterranean fruit fly Ceratitis capitata, the Vinegar fly Drosophila melanogaster and the housefly Musca domestica. Flies were raised in different temperature and density regimes that allowed us to study the effects of these environmental factors on wing shape. Additionally, in accordance with different mating behaviors of these flies, we observed a clear sexual shape dimorphism in all three species. Since the three studied species represent serious pests and disease vectors, our findings may contribute to existing and future monitoring efforts.

zoology

De Novo Assembly And Annotation Of The Eastern Fence Lizard (Sceloporus undulatus) Transcriptome

BackgroundThe eastern fence lizard (Sceloporus undulatus) has been a model species for ecological and evolutionary research. Genomic and transcriptomic resources for this species would promote investigation of genetic mechanisms that underpin plastic responses to environmental stress, such as climate warming. Moreover, such resources would aid comparative studies of complex traits at the molecular level, such as the transition from oviparous to viviparous reproduction, which happened at least four times within Sceloporus.\n\nFindingsA de novo transcriptome assembly for Sceloporus undulatus, Sund_v1.0, was generated using over 179 million Illumina reads obtained from three tissues (whole brain, skeletal muscle, and embryo) as well as previously reported liver sequences. The Sund_v1.0 assembly had an average contig length of 782 nucleotides and an E90N50 statistic of 2,550 nucleotides. Comparing S. undulatus transcripts with the benchmarking universal single-copy orthologs (BUSCO) for tetrapod species yielded 97.2% gene representation. A total of 13,422 protein-coding orthologs were identified in comparison to the genome of the green anole lizard, Anolis carolinensis, which is the closest related species with genomic data available.\n\nConclusionsThe multi-tissue transcriptome of S. undulatus is the first for a member of the family Phrynosomatidae, offering an important resource to advance studies of adaptation in this species and genomic research in reptiles.

genomics

Coalescent Processes With Skewed Offspring Distributions And Non-Equilibrium Demography

Non-equilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a non-linear change of time scale - analogous to the Kingman coalescent - we find that the ancestral process can be rescaled to its time-homogeneous analogue, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately given linkage equilibrium, while linkage disequilibrium systematically biases growth rate estimates. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.

evolutionary biology

Comparative Genomics Sheds Light On Niche Differentiation And The Evolutionary History Of Comammox Nitrospira

The description of comammox Nitrospira spp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria ({beta}-AOB) in the environment, call into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonium oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira.\n\nComammox Nitrospira has lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizing Nitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to other Nitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to {beta}-AOB, comammox Nitrospira genomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammox Nitrospira seems attuned to oligotrophy and hypoxia compared to {beta}-AOB.\n\n{beta}-AOBs are the clear origin of the ammonium oxidation pathway in comammox Nitrospira: reconciliation analysis indicates two separate early amoA gene transfer events from {beta}-AOB to an ancestor of comammox Nitrospira, followed by clade specific losses. For haoA, one early transfer from {beta}-AOB to comammox Nitrospira is predicted - followed by intra-clade transfers. We postulate that the absence of comammox genes in most Nitrospira genomes is the result of subsequent loss.\n\nSignificanceThe recent discovery of comammox bacteria - members of the Nitrospira genus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammox Nitrospira and related nitrifiers. Ammonium oxidation genes in comammox Nitrospira had a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.

microbiology