Biology subjects

Mills, S.

Publications and source records attributed to Mills, S..

15 recordsLinked to original sources

bioRxiv2026

TGF-β- and IL-1-dependent fibroblast states differentially shape pancreatic cancer microenvironments and metastasis

Pancreatic ductal adenocarcinoma (PDAC) contains heterogeneous cancer-associated fibroblast (CAF) populations, including interleukin 1 (IL-1)-dependent inflammatory CAFs (iCAFs) and transforming growth factor beta (TGF-{beta})-dependent myofibroblastic CAFs (myCAFs), whose functions at primary and metastatic sites remain incompletely defined. Here, we genetically disrupted IL-1 or TGF-{beta} signalling in fibroblast activation protein (FAP)-expressing CAFs arising from a shared cellular origin to determine how myCAF and iCAF states shape PDAC progression and microenvironments. Depletion of TGF-{beta}-dependent myCAFs, but not IL-1-dependent iCAFs, did not alter primary tumour growth or local metastatic dissemination but significantly reduced liver and lung metastases. Matched primary tumours and liver metastasis analyses also revealed site-specific stromal responses to TGF-{beta} signalling disruption. Experimental models of liver metastasis colonisation and outgrowth indicated that the reduced metastatic phenotype was linked primarily to alterations within pancreatic tumours rather than to impaired malignant cell outgrowth at metastatic sites. Single-cell RNA-sequencing of myCAF-depleted primary tumours revealed extensive transcriptional reprogramming across fibroblast, immune and malignant compartments, highlighting the complexity of assigning myCAF-to-malignant cell signalling mechanisms in vivo. To resolve this crosstalk, we co-cultured PDAC organoids with pancreatic stellate cells engineered to remain in myCAF or iCAF states. Cross-model transcriptomic analyses, together with genetic and pharmacological perturbation studies, showed that myCAF-derived TGF-{beta} directly promotes epithelial-to-mesenchymal transition signalling in PDAC malignant cells, providing a candidate mechanism for the reduced metastasis observed upon myCAF depletion in vivo. These findings reveal distinct, context-dependent roles for TGF-{beta}- and IL-1-dependent CAF states and identify myCAF-derived TGF-{beta} signalling as a stromal mechanism promoting malignant cell plasticity.

cancer biology↗

bioRxiv2026

Chilling injury to algal symbionts induces host starvation and metabolic reorganization in a temperate cnidarian

Global temperature anomalies increasingly disrupt the cnidarian-algal symbiosis through a phenomenon termed bleaching. In contrast to heat stress, the mechanisms underlying symbiotic breakdown under cold stress remain largely unknown. Combining physiological and metabolomic measurements, we investigated the response of the photosymbiotic sea anemone holobiont Aiptasia couchii to an experiment mimicking a cold spell in the Mediterranean Sea. Within four weeks, we observed the onset of symbiotic breakdown reflected in reduced algal endosymbiont density and chlorophyll a content. While photosynthetic efficiency remained largely unaffected, no gross photosynthesis was detectable in cold-stressed anemones and decreases in glycosyldiacylglycerols and fatty acyl glycosides indicated chloroplast lipid remobilization. This breakdown of symbiotic carbon cycling was reflected in increased dipeptide and ceramide levels suggesting anemones catabolized protein reserves and induced pre-apoptotic pathways. Taken together, these responses suggest a decoupling of light and dark reactions of photosynthesis in cold-stressed endosymbionts, resembling chilling injury in higher plants and free-living microalgae. This chilling-induced collapse of symbiotic nutrient cycling eventually leads to host starvation in cold-stressed Cnidaria. Hence, while cold and heat stress may invoke contrasting physiological effects on endosymbionts, our results suggest that both stressors destabilize the symbiosis through similar mechanisms culminating in host starvation.

ecology↗

bioRxiv2026

Persistent declines in forest-dependent birds following active restoration of logged tropical forest in Borneo

O_LITropical forest restoration is critical for mitigating biodiversity loss and climate change, including in forests impacted by selective logging. Active restoration through liana cutting and enrichment tree planting can substantially accelerate carbon recovery, potentially reducing economic pressures to convert logged forests. But its long-term biodiversity impacts remain largely unknown. C_LIO_LIUsing over two decades of bird survey data from Borneos largest logged-forest restoration project, we quantified occupancy patterns for 176 species across primary, naturally regenerating, and actively restored logged forests spanning a 30+ year post-logging chronosequence. C_LIO_LIForest-dependent, threatened and near-threatened species generally declined through time in actively restored areas, whereas many species in naturally regenerating forests progressively recovered toward primary forest levels. Between 17-40% of 66 threatened or near-threatened species had consistently lower occupancies in actively restored than in naturally regenerating forest. Across species of global conservation concern, median occupancies in restored areas remained [~]22% below primary forest even 50 years after harvests, compared with only [~]6% lower under natural regeneration. C_LIO_LIArboreal insectivores, frugivores, and predatory species appeared most negatively affected by active restoration, with 27-49% of arboreal gleaning insectivores (of 62), 13-30% of arboreal frugivores (of 40), and one-third of predatory species (of 15) showing higher occupancy in naturally regenerating forests. Sallying insectivores also showed a possible but uncertain response, whereas ground-associated frugivores and insectivores were largely unaffected by restoration treatment. C_LIO_LIConcerningly, even 50 years post-logging, up to 52% of 50 high forest-dependency species retained distinct occupancies in actively restored compared with primary forest, suggesting persistent negative impacts of vine-cutting and/or tree planting activities on avian populations. C_LIO_LISynthesis and applications. Our findings indicate that despite substantial carbon benefits, active restoration within selectively logged forests may impede the recovery of forest-dependent biodiversity. This challenges the common assumption embedded within nature-based climate solutions that carbon and biodiversity outcomes will necessarily align. Nonetheless, despite the persistent declines in bird communities, actively restored forests continued to provide key habitat for many species. Active interventions may thus still contribute to broader biodiversity conservation objectives if they protect logged areas from conversion, potentially via carbon payments. C_LI

ecology↗

bioRxiv2026

Cross-species graph-embedding unmasks the ageing microenvironment as a key determinant of pancreatic cancer malignant cell biology and therapy response

Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis and is characterised by an extensive pro-tumorigenic stroma. Although most PDAC cases occur in older patients, the impact of ageing on malignant-stromal interactions and therapy response remains poorly understood. Here, we established orthotopically-grafted organoid-derived PDAC models across three murine age groups to characterise changes in the PDAC stroma and malignant cells with ageing. Cross-species analyses of tumour transcriptomes using a graph-embedding approach showed that integrating mouse models of different ages better captures the diversity of human PDAC, and that aged models more faithfully recapitulate the biology of older patients with PDAC. We also demonstrated that aged PDAC models have a more inflammatory stroma than that of younger tumours, shaping the malignant cell transcriptome. Finally, graph-embedding identified IRAK4 as a candidate therapeutic vulnerability in aged, but not young, KRAS- and p53-mutant PDAC, which we validated in preclinical drug studies. These findings highlight how ageing is a critical determinant of PDAC biology and associated therapeutic vulnerabilities, which should be an important consideration when designing disease models for preclinical development of precision therapies.

cancer biology↗

bioRxiv2025

Multi-stromal organoid co-cultures model pancreatic cancer and pancreatitis epithelial cell-fibroblast heterogeneity

Malignant cell-fibroblast cross-talks modulate disease progression and therapy response of pancreatic ductal adenocarcinoma (PDAC). Our knowledge of the heterogeneous nature of PDAC cancer-associated fibroblasts (CAFs) has significantly increased over the last few years. Yet, whether CAFs in PDAC differ from fibroblasts in pancreatic inflammation remains poorly understood. Chronic pancreatitis - a prolonged inflammatory state of the pancreas - is a risk factor for PDAC and is characterised by abundant fibroblasts. Thus, dissecting pancreatic fibroblast and epithelial cell reprogramming in malignancy relative to inflammation could inform new preventative, diagnostic and therapeutic strategies for PDAC. Here, we studied how pancreatic malignancy and inflammation differently shape fibroblast heterogeneity and their crosstalk with epithelial cells. We analysed human samples and mouse models of pancreatitis and PDAC and leveraged new murine pancreatitis-derived epithelial organoids to establish pancreatitis and PDAC organoid/multi-stroma co-cultures comprising pancreatic stellate cells, fibroblasts and mesothelial cells. We demonstrate that a combination of in vitro and in vivo models better captures epithelial cell and fibroblast markers of human pancreatitis and PDAC compared to mouse models alone. Finally, we identify PDAC and pancreatitis epithelial cell-specific reprogramming of stromal cells of different origin, and we infer the contribution of these distinct stromal cell types to fibroblasts in PDAC and pancreatitis in vivo. Together, our study highlights different epithelial cell-fibroblast heterogeneity in PDAC and pancreatitis, and provides new platforms for the identification of markers and epithelial-stromal interdependencies of these diseases.

cancer biology↗

bioRxiv2025

Molecular evolution of CO2-sensing ab1C neurons underlies divergent sensory responses in the Drosophila suzukii species group

Organisms evolve behavioral and morphological traits to adapt to their ecological niches, yet the genetic basis of adaptation remains largely unknown. Drosophila suzukii has evolved a distinctive oviposition preference for ripe fruit, unlike most Drosophila species such as D. melanogaster, which prefer overripe fruit. Carbon dioxide (CO2), a metabolic volatile that increases as fruit ripens and decays, may act as a critical ecological cue shaping these preferences. Here, we focus on D. suzukii and its sister species D. subpulchrella, which shows an intermediate preference, to investigate the genetic basis of CO2 responses. We report a previously unrecognized shift in CO2-guided oviposition: D. suzukii and D. subpulchrella readily lay eggs on CO2-enriched substrates, unlike the strong aversion displayed by D. melanogaster. Electrophysiological recordings revealed a species-specific sensory tuning, characterized by an early spike in CO2-evoked neuronal firing in D. suzukii and D. subpulchrella--a temporal response feature absent in D. melanogaster. To dissect the genetic basis of this shift, we generated transgenic D. melanogaster expressing either the D. suzukii Gr63a coding sequence or the D. subpulchrella Gr63a cis-regulatory element. Remarkably, both manipulations reproduced the early onset firing pattern of CO2 sensitivity, demonstrating that either receptor function or expression can independently drive this sensitivity adaptation. Our findings reveal that evolution can shape ecological adaptation through distinct genetic mechanisms, leading to convergent physiological traits among closely related species. Author SummaryAnimals rely on their senses to locate food sources and identify suitable reproductive sites in their environment. Closely related species can evolve strikingly different preferences as they adapt to new environments. For example, the invasive fruit fly D. suzukii lays its eggs in ripe fruit, unlike most other fruit flies, such as D. melanogaster, which prefer decaying fruit. Because CO2 levels increase as fruit ripens and ferments, changes in how flies detect CO2 may have contributed to these ecological differences. We compared CO2 responses between D. suzukii and its sister species D. subpulchrella, and found that both species respond to CO2 differently from D. melanogaster: both in their oviposition preferences and neural CO2 sensitivity. By introducing either the D. subpulchrella or D. suzukii CO2 receptor gene coding sequences or regulatory regions into D. melanogaster, we found that this altered sensitivity can arise from changes either in the receptors protein-coding region or in the DNA elements that control its expression. Our results show that evolution can act through multiple genetic mechanisms to fine-tune sensory systems, revealing how subtle molecular changes can generate ecological diversity among closely related species.

evolutionary biology↗

bioRxiv2025

Unexpected diversity of Isidoides (Anthozoa: Octocorallia: Isidoidae) revealed by morphology and phylogenomics analysis with descriptions of four new species

Isidoidae Heestand Saucier, France & Watling, 2021 is a rare octocoral family currently represented by a single genus and species, Isidoides armata Nutting, 1910 recorded in the western Pacific Ocean. The taxonomic status and diversity of Isidoides is unclear, due to the lack of diagnostic taxonomic features and limited taxon sampling. Based on 23 Isidoides specimens obtained from the northwestern to southwestern Pacific, we carried out morphological and phylogenetic analyses to reveal the taxonomic status of new species and develop reliable features for species identification. The 23 specimens could be classified into four well-supported clades by the phylogenomic analysis of ultraconserved elements (UCEs), four groups by 28S rDNA, and two groups by mtMutS-cox1. Integrating morphology and molecular data, we uncovered unexpected diversity of Isidoides composed of the known species Isidoides armata and three new species, viz., I. elegans sp. nov., I. gracilis sp. nov. and I. pseudarmata sp. nov. The morphological analysis showed high intraspecific morphological variation in colony color and the size, shape and arrangement of polyps. By contrast, sclerite forms with their surface sculpturing are more diagnostic features for species identification. Our phylogenetic and species delimitation analyses indicate that UCEs have higher resolution than the nuclear 28S rDNA and the mitochondrial genes mtMutS and cox1 for species discrimination within Isidoidae. ZooBank: urn:lsid:zoobank.org:pub:392485F5-502E-4383-B153-45B167571190

zoology↗

bioRxiv2025

Recovering historical fish eDNA from museum-preserved Antarctic filter feeders via non-destructive metabarcoding.

O_LIRecent technical advances have significantly enhanced the value of museum specimens for molecular research, with metagenomic and metabarcoding approaches expanding further the utility of museum collections. However, given the finite number of specimens, there is a critical need to move past destructive DNA extraction approaches and to explore non-destructive techniques. C_LIO_LIIn this study, we evaluated the feasibility of extracting historical fish eDNA from the ethanol preservative used to store Antarctic museum specimens. We compared a variety of extraction methods - centrifugation, evaporation, filtration, and precipitation - using ten replicate samples per treatment for statistical analyses. To assess potential differences in preservative-derived eDNA recovery across different filter-feeding taxonomic groups, we included a Bryozoa and two Porifera, i.e., Demospongiae and Hexactinellida. C_LIO_LIComparative analyses with tissue biopsies revealed that the total genomic DNA was significantly reduced for non-destructive approaches. However, 10 ml ethanol filtration performed equal to, or in some instances, outperformed tissue biopsies when investigating the historical eDNA of Antarctic fish using a 16S rRNA metabarcoding approach, both for the number of species detected (-diversity) and community characterisation ({beta}-diversity). C_LIO_LIOur findings demonstrate the potential of ethanol preservative as a valuable, non-destructive source of historical fish eDNA from museum-stored filter-feeding specimens. These results highlight the viability of non-destructive sampling for molecular research on museum collections, preserving specimen integrity while enabling biodiversity assessments. Further refinement of non-destructive eDNA extraction could expand its applicability across taxa, collection types, and preservation methods, ensuring the long-term sustainability of museum-based genomic research. C_LI

ecology↗

bioRxiv2024

Dissolved organic matter fluxes and fatty acid composition from shallow-water and deep-water demo- and hexactinellid sponges from New Zealand

Sponges are an important component of shallow- and deep-water ecosystems enhancing eukaryotic biodiversity via diverse endo- and epibiota and by providing three dimensional habitats for benthic invertebrates and fishes. Sponge biodiversity is particularly high in the waters around New Zealand (Southwest Pacific), where we collected two shallow- and two deep-water sponge species (Tedania sp., Suberea meandrina, Farrea raoulensis, Artemisina sp.) for ex-situ incubation experiments to detect whether these sponges may process dissolved organic matter. We assessed the biochemical and phospholipid-derived fatty acids (PLFAs) and measured dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) fluxes. Changes in fluorescent dissolved organic matter (FDOM) over time were analyzed and the results were linked to the bacterial communities of the sponge holobiont. Dried sponge tissue consisted of 17.5 {+/-} 3.75% organic (org.) C and of 4.34 {+/-} 1.02% total nitrogen (TN) with a natural stable isotope composition of -19.0 {+/-}0.25{per thousand} for {delta}13org. C and of 10.2 {+/-}2.43{per thousand} for {delta}15TN. None of the DOC fluxes was significant and only the release of TDN by Tedania sp. was significantly different from 0 mol TDN g org. C-1 d-1. We detected the presence of four fluorophores in the FDOM pool: 2 tryptophan- and protein-like fluorophores (C1, C2), 1 humic-like fluorophore (C3), and 1 tyrosine-like fluorophore (C4). The maximum fluorescence intensity Fmax of C1 decreased significantly in S. meandrina incubations, whereas Fmax of C2 grew in the same incubations. Fmax of C3 increased in Tedania sp. incubations, in which Fmax of C4 decreased. In comparison, Fmax of C4 in S. meandrina rose. The PLFA composition of sponge tissue was dominated by long-chain fatty acids, saturated fatty acids, and monosaturated fatty acids and most PLFAs were sponge- and bacteria-specific. The bacterial community of the demosponges Artemisina sp., S. meandrina and Tedania sp. consisted mostly of Proteobacteria and Chloroflexota, whereas the dominating bacteria phylum of the hexactinellid F. raoulensis was Proteobacteria. We proposed that the holobionts of S. meandrina and Tedania sp. contain bacteria that are involved in the transformation and degradation of DOM. In S. meandrina, Chloroflexota and Poribacteria may degrade tryptophan-like fluorophores to a chemically modified tryptophan-like and protein-like fluorophore, while producing a tyrosine-like fluorophore. In Tedania sp., Chloroflexota may contribute to the release of significant amounts of TDN by producing humic-like fluorophores, while degrading tyrosine-like fluorophores. Farrea raoulensis may not take up DOM due to a lack of Poribacteria and Chloroflexota or may use colloidal instead of truly dissolved DOC.

ecology↗

bioRxiv2024

A Human iPSC-derived Organoid System to Model Myelin Destruction and Repair

We engineered a novel human iPSC-derived organoid system enriched with mature, myelinating oligodendrocytes and functionally reactive microglia. This model enables the study of human CNS remyelination following a demyelinating insult, encapsulating: myelin fragmentation, microglial clearance of myelin debris and oligodendrocyte genesis, differentiation, and axon ensheathment. This system provides a powerful and unparalleled capacity to interrogate complex human cell behaviour, relevant to those studying glial biology and neurological disease mechanisms.

neuroscience↗

bioRxiv2024

Nutrient fluxes, oxygen consumption and fatty acid composition from deep-water demo- and hexactinellid sponges from New Zealand

Sponges are an important component of deep-water ecosystems enhancing eukaryotic biodiversity by hosting diverse endo- and epibiota and providing three dimensional habitats for benthic invertebrates and fishes. As holobionts they are important hosts of microorganisms which are involved in carbon and nitrogen cycling. While increasing exploration of deep-water habitats results in new sponge species being discovered, little is known about their physiology and role in nutrient fluxes. Around New Zealand (Southwest Pacific), the sponge biodiversity is particularly high, and we selected six deep-sea sponge clusters (Saccocalyx, Suberites, Tedania, Halichondria/ Dendoricella, Sceptrulophora, Lissodendoryx) for in-situ and ex-situ experiments. We investigated the biochemical composition of the sponges, measured oxygen consumption and inorganic nutrient fluxes, as well as bacterial and phospholipid-derived fatty acid (PLFA) compositions. Our aim was to assess differences in fluxes and fatty acid composition among sponge clusters and linking their bacterial communities to nitrogen cycling processes. All sponges excreted nitrite and ammonia. Nitrate and phosphate excretion were independent of phylum affiliation (Demospongiae, Hexactinellida). Nitrate was excreted by the Halichondria/ Dendoricella and Lissodendoryx clusters, whereas the Suberites, Tedania, and Sceptrulophora clusters consumed it. Phosphate was excreted by Sceptrulophora and Halichondria/ Dendoricella clusters and consumed by all other clusters. Silicon was consumed by all sponge clusters, except for Saccocalyx and Halichondria/ Dendoricella clusters. Oxygen consumption rates ranged from 0.17 to 3.56{+/-}0.60 mmol O2 g C d-1. The PLFA composition was very sponge-cluster dependent and consisted mostly of long-chain fatty acids. Most PLFAs were sponge-specific, followed by bacteria-specific PLFAs, and others. All sponge clusters, except for Suberites, were low-microbial abundance (LMA) sponges whose bacterial community composition was dominated by Proteobacteria, Bacteroidota, Planctomycetota, and Nitrospinota. The Suberites cluster consisted of high-microbial abundance (HMA) sponges with Proteobacteria, Chloroflexota, Acidobacteriota, and Actinobacteriota as dominant bacteria. Based on the inorganic nitrogen flux measurements, we identified three types of nitrogen cycling in the sponges: In type 1, sponges (Dendoricella spp. indet., Lissodendoryx cluster) respired aerobically and ammonificated organic matter (OM) to ammonium, fixed N2 to ammonium, and nitrified aerobically heterotrophically produced ammonium to nitrate and nitrite. In type 2, sponges (Halichondria sp., Sceptrulophora, Suberites, Tedania clusters) respired OM aerobically and ammonificated it to ammonium. They also reduced nitrate anaerobically to ammonium via dissimilatory nitrate reduction to ammonium. In type 3, ammonium was microbially nitrified to nitrite and afterwards to nitrate presumably by ammonium-oxidizing Bacteria and/ or Archaea.

ecology↗

bioRxiv2024

Unlocking Antarctic molecular time-capsules - recovering historical environmental DNA from museum-preserved sponges

Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA (heDNA), trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.

molecular biology↗

bioRxiv2024

Phylogenomics reveals coincident divergence between giant host sea anemones and the clownfish adaptive radiation.

The mutualism between clownfishes (or anemonefishes) and their giant host sea anemones are among the most immediately recognizable animal interactions on the planet and have attracted a great deal of popular and scientific attention [1-5]. However, our evolutionary understanding of this iconic symbiosis comes almost entirely from studies on clownfishes-- a charismatic group of 28 described species in the genus Amphiprion [2]. Adaptation to venomous sea anemones (Anthozoa: Actiniaria) provided clownfishes with novel habitat space, ultimately triggering the adaptive radiation of the group [2]. Clownfishes diverged from their free-living ancestors 25-30 MYA with their adaptive radiation to sea anemones dating to 13.2 MYA [2, 3]. Far from being mere habitat space, the host sea anemones also receive substantial benefits from hosting clownfishes, making the mutualistic and co-dependent nature of the symbiosis well established [4, 5]. Yet the evolutionary consequences of mutualism with clownfishes have remained a mystery from the host perspective. Here we use bait-capture sequencing to fully resolve the evolutionary relationships among the 10 nominal species of clownfish-hosting sea anemones for the first time (Figure 1). Using time-calibrated divergence dating analyses we calculate divergence times of less than 25 MYA for each host species, with 9 of 10 host species having divergence times within the last 13 MYA (Figure 1). The clownfish-hosting sea anemones thus diversified coincidently with clownfishes, potentially facilitating the clownfish adaptive radiation, and providing the first strong evidence for co-evolutionary patterns in this iconic partnership. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/576469v1_fig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@7053b4org.highwire.dtl.DTLVardef@876c65org.highwire.dtl.DTLVardef@dd6d9forg.highwire.dtl.DTLVardef@147fddd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Diversification of the clownfish-hosting sea anemones was coincident with the clownfish adaptive radiation. A) Time-calibrated maximum likelihood cladogram of Order Actiniaria based on 328 ultra-conserved element and exon loci (75% data occupancy matrix). The three clades containing the clownfish hosting sea anemones are highlighted reflecting the multiple evolutionary origins of symbiosis with clownfishes within superfamily Actinioidea. B-D) Detailed time-calibrated maximum likelihood cladograms of Entacmaea quadricolor, Clade Stichodactylina, and Clade Heteractina, respectively. In all panels, the orange line denotes the beginning of the clownfish adaptive radiation 13 MYA. Sea anemone superfamilies Actinostoloidea, Metridioidea, Actiniernoidea, and Edwardsioidea are collapsed for clarity. C_FIG

evolutionary biology↗

bioRxiv2019

De Novo Growth Of Methanogenic Granules Indicates A Biofilm Life-Cycle With Complex Ecology

Methanogenic sludge granules are densely packed, small (diameter, approx. 0.5-2.0 mm) spherical biofilms found in anaerobic digesters used to treat industrial wastewaters, where they underpin efficient organic waste conversion and biogas production. A single digester contains millions of individual granules, each of which is a highly-organised biofilm comprised of a complex consortium of likely billions of cells from across thousands of species - but not all granules are identical. Whilst each granule theoretically houses representative microorganisms from all of the trophic groups implicated in the successive and interdependent reactions of the anaerobic digestion process, parallel granules function side-by-side in digesters to provide a meta-organism of sorts. Granules from a full-scale bioreactor were size-separated into small, medium and large granules. Laboratory-scale bioreactors were operated using only small (0.6-1 mm), medium (1-1.4 mm) or large (1.4-1.8 mm) granules, or unfractionated (naturally distributed) sludge. After >50 days of operation, the granule size distribution in each of the small, medium and large bioreactor types had diversified beyond - to both bigger and smaller than - the size fraction used for inoculation. New granules were analysed by studying community structure based on high-throughput 16S rRNA gene sequencing. Methanobacterium, Aminobacterium, Propionibacteriaceae and Desulfovibrio represented the majority of the community in new granules. H2-using, and not acetoclastic, methanogens appeared more important, and were associated with abundant syntrophic bacteria. Multivariate integration analyses identified distinct discriminant taxa responsible for shaping the microbial communities in different-sized granules, and along with alpha diversity data, indicated a possible biofilm life cycle.\n\nImportanceMethanogenic granules are spherical biofilms found in the built environment, where despite their importance for anaerobic digestion of wastewater in bioreactors, little is understood about the fate of granules across their entire life. Information on exactly how, and at what rates, methanogenic granules develop will be important for more precise and innovative management of environmental biotechnologies. Microbial aggregates also spark interest as subjects in which to study fundamental concepts from microbial ecology, including immigration and species sorting affecting the assembly of microbial communities. This experiment is the first, of which we are aware, to compartmentalise methanogenic granules into discrete, size-resolved fractions, which were then used to separately start up bioreactors to investigate the granule life cycle. The evidence, and extent, of de novo granule growth, and the identification of key microorganisms shaping new granules at different life-cycle stages, is important for environmental engineering and microbial ecology.

microbiology↗

bioRxiv2018

Diversity Converges During Community Assembly In Methanogenic Granules, Suggesting A Biofilm Life-Cycle

Anaerobic biological decomposition of organic matter is ubiquitous in Nature wherever anaerobic environments prevail, and is catalysed by hydrolytic, fermentative, acetogenic, methanogenic, and various other groups, including syntrophic bacteria. It is also harnessed in innovative ways in engineered systems that may rely on small (0.1-4.0 mm), spherical, anaerobic granules, which we have found to be highly-replicated, whole-ecosystems harbouring the entire community necessary to mineralise complex organics. We hypothesised distinct granule sizes correspond to stages in a biofilm life-cycle, in which small granules are young and larger ones are old. Here, granules were separated into 10 size fractions used for physico-chemical and ecological characterisation. Gradients of volatile solids, density, settleability, biofilm morphology, methanogenic activity, and EPS profiles were observed across size fractions. Sequencing of 16S rRNA genes indicated linear convergence of diversity during community assembly as granules increased in size. A total of 155 discriminant OTUs were identified, and correlated strongly with physico-chemical parameters. Community assembly across sizes was influenced by a niche effect, whereby Euryarchaeota dominated a core microbiome presumably as granules became more anaerobic. The findings indicate opportunities for precision management of environmental biotechnologies, and the potential of aggregates as playgrounds to study assembly and succession in whole microbiomes.

microbiology↗