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We evaluated the impact of an HIV prevention intervention combining street outreach, storefront prevention services, and subculture-specific activities, for homeless, runaway, and street youth. Using systematic, street-based sampling techniques, we conducted 1,146 interviews in cross-sectional surveys at intervention and comparison sites prior to and during intervention implementation. Youth in both sites reported high rates of risky sexual and injection drug use behaviors. In logistic regression the intervention did not impact HIV risk behaviors, but was independently associated with increased outreach worker (OW) contact and referrals for services. Higher levels of OW contact were associated with following through with HIV-related referrals and using new syringes. Youth-oriented needle exchange increased use of new syringes. While our study did not demonstrate an intervention effect on HIV risk behaviors, intensive, subculture-specific outreach, including needle exchange, may improve the lives of street youth. [ABSTRACT FROM AUTHOR]

Objectives: The central challenge in third-generation sequencing lies in meeting the requirements for DNA quality (integrity and purity) and quantity. Therefore, novel improvements in DNA extraction methods are needed to satisfy these requirements. We reasoned that in anaerobic microbial communities, the presence of certain strict anaerobes containing oxygen-activated DNase activity might contribute substantially to the poor integrity of extracted metagenomic DNA (or genomic DNA from some pure cultures) if exposed to air., Methods: To test this hypothesis, we developed an enhanced genomic and metagenomic DNA isolation technique that we applied to a specifically chosen set of both strict and aerotolerant anaerobes, as well as to the hindgut microbiota of a herbivorous marine fish., Results: Considering the quality (or degradation) of extracted DNA obtained under anaerobic versus aerobic conditions, we found that DNA extracted aerobically from cells of some strict anaerobes showed more degradation of high molecular weight DNA than analogous preparations under anaerobic conditions. In contrast, with the selected aerotolerant anaerobes, no discernible difference was found between the molecular sizes of DNA extracted aerobically and anaerobically. Metagenomic DNA extracted from the fish hindgut microbiota showed higher yields and better quality under anaerobic conditions compared to aerobic conditions., Conclusion: Our study effectively demonstrates the advantages of our improved extraction protocol in anaerobic conditions. This is evident through the improved quality of extracted DNA. Such findings may be valuable for studies, especially metagenomic studies, where the quality and quantity of DNA are crucial for downstream analysis., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The gut microbiota of the marine herbivorous fish Kyphosus sydneyanus are thought to play an important role in host nutrition by supplying short-chain fatty acids (SCFAs) through fermentation of dietary red and brown macroalgae. Here, using 645 metagenome-assembled genomes (MAGs) from wild fish, we determined the capacity of different bacterial taxa to degrade seaweed carbohydrates along the gut. Most bacteria (99%) were unclassified at the species level. Gut communities and CAZyme-related transcriptional activity were dominated by Bacteroidia and Clostridia . Both classes possess genes CAZymes acting on internal polysaccharide bonds, suggesting their role initiating glycan depolymerization, followed by rarer Gammaproteobacteria and Verrucomicrobiae . Results indicate that Bacteroidia utilize substrates in both brown and red algae, whereas other taxa, namely, Clostridia , Bacilli , and Verrucomicrobiae , utilize mainly brown algae. Bacteroidia had the highest CAZyme gene densities overall, and Alistipes were especially enriched in CAZyme gene clusters ( n  = 73 versus just 62 distributed across all other taxa), pointing to an enhanced capacity for macroalgal polysaccharide utilization (e.g., alginate, laminarin, and sulfated polysaccharides). Pairwise correlations of MAG relative abundances and encoded CAZyme compositions provide evidence of potential inter-species collaborations. Co-abundant MAGs exhibited complementary degradative capacities for specific substrates, and flexibility in their capacity to source carbon (e.g., glucose- or galactose-rich glycans), possibly facilitating coexistence via niche partitioning. Results indicate the potential for collaborative microbial carbohydrate metabolism in the K. sydneyanus gut, that a greater variety of taxa contribute to the breakdown of brown versus red dietary algae, and that Bacteroidia encompass specialized macroalgae degraders., Competing Interests: The authors declare that they have no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Fish biologists have long assumed a link between intestinal length and diet, and relative gut length or Zihler's index are often used to classify species into trophic groups. This has been done for specific fish taxa or specific ecosystems, but not for a global fish dataset. Here, we assess these relationships across a dataset of 468 fish species (254 marine, 191 freshwater, and 23 that occupy both habitats) in relation to body mass and fish length. Herbivores had significantly relatively stouter bodies and longer intestines than omni- and faunivores. Among faunivores, corallivores had longer intestines than invertivores, with piscivores having the shortest. There were no detectable differences between herbivore groups, possibly due to insufficient understanding of herbivorous fish diets. We propose that reasons for long intestines in fish include (i) difficult-to-digest items that require a symbiotic microbiome, and (ii) the dilution of easily digestible compounds with indigestible material (e.g., sand, wood, exoskeleton). Intestinal indices differed significantly between dietary groups, but there was substantial group overlap. Counter-intuitively, in the largest dataset, marine species had significantly shorter intestines than freshwater fish. These results put fish together with mammals as vertebrate taxa with clear convergence in intestine length in association with trophic level, in contrast to reptiles and birds, even if the peculiar feeding ecology of herbivorous fish is probably more varied than that of mammalian herbivores., Supplementary Information: The online version contains supplementary material available at 10.1007/s11160-024-09853-3., Competing Interests: Conflict of interestThe authors declare no conflict of interest., (© The Author(s) 2024.)

A Gram-stain-negative, non-spore-forming, rod-shaped, obligately anaerobic bacterium, designated strain BP5G T , was isolated from the hindgut of a silver drummer ( Kyphosus sydneyanus ) fish collected from the Hauraki Gulf, New Zealand. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belonged to the family Lachnospiraceae in the phylum Bacillota and was most closely related to Anaerotignum propionicum with 94.06 % sequence identity. Isolate BP5G T grew on agar medium containing mannitol and fish gut fluid as carbon sources. Clear colonies of approximately 1 mm diameter of the isolate grew within a week at 20-28 °C (optimum, 28 °C) and pH 7.6-8.5 (optimum, pH 8.5). Strain BP5G T was very sensitive to NaCl and the optimal concentration for growth was 0.045 % (w/v). Acetate and propionate were the major fermentation products. The major cellular fatty acids were C 12 : 0 , C 14 : 0 , C 15 : 0 and C 16 : 0 . The genome sequence of the isolate was determined. Its G+C content was 38.41 mol% and the 71.41 % average nucleotide identity of the BP5G T genome to its closest neighbour with a sequenced genome ( A. propionicum DSM 1682 T ) indicated low genomic relatedness. Based on the phenotypic and taxonomic characteristics observed in this study, a novel genus and species named Chakrabartyella piscis gen. nov., sp. nov. is proposed for isolate BP5G T (=ICMP 24687 T =JCM 35769 T ).

Background: Gut microbiota play a key role in the nutrition of many marine herbivorous fishes through hindgut fermentation of seaweed. Gut microbiota composition in the herbivorous fish Kyphosus sydneyanus (family Kyphosidae) varies between individuals and gut sections, raising two questions: (i) is community composition stable over time, especially given seasonal shifts in storage metabolites of dietary brown algae, and (ii) what processes influence community assembly in the hindgut?, Results: We examined variation in community composition in gut lumen and mucosa samples from three hindgut sections of K. sydneyanus collected at various time points in 2020 and 2021 from reefs near Great Barrier Island, New Zealand. 16S rRNA gene analysis was used to characterize microbial community composition, diversity and estimated density. Differences in community composition between gut sections remained relatively stable over time, with little evidence of temporal variation. Clostridia dominated the proximal hindgut sections and Bacteroidia the most distal section. Differences were detected in microbial composition between lumen and mucosa, especially at genus level., Conclusions: High variation in community composition and estimated bacterial density among individual fish combined with low variation in community composition temporally suggests that initial community assembly involved environmental selection and random sampling/neutral effects. Community stability following colonisation could also be influenced by historical contingency, where early colonizing members of the community may have a selective advantage. The impact of temporal changes in the algae may be limited by the dynamics of substrate depletion along the gut following feeding, i.e. the depletion of storage metabolites in the proximal hindgut. Estimated bacterial density, showed that Bacteroidota has the highest density (copies/mL) in distal-most lumen section V, where SCFA concentrations are highest. Bacteroidota genera Alistipes and Rikenella may play important roles in the breakdown of seaweed into useful compounds for the fish host., (© 2023. BioMed Central Ltd., part of Springer Nature.)

The intestinal microbiota contributes to energy metabolism, but the molecular mechanisms involved remain less clear. Bacteria of the genus Bacillus regulate lipid metabolism in the host and are thus commonly used as beneficial probiotic supplements. In the present study, Bacillus licheniformis FA6 was selected to assess its role in modulating lipid metabolism of zebrafish ( Danio rerio ). Combining 16S rRNA high-throughput sequencing, micro-CT scan, metabolic parameters measurement, and gene expression analysis, we demonstrated that B. licheniformis FA6 changed the gut microbiota composition of zebrafish and increased both the Firmicutes/Bacteroidetes ratio and lipid accumulation. In terms of metabolites, B. licheniformis FA6 appeared to promote acetate production, which increased acetyl-CoA levels and promoted lipid synthesis in the liver. In contrast, addition of B. licheniformis lowered carnitine levels, which in turn reduced fatty acid oxidation in the liver. At a molecular level, B. licheniformis FA6 upregulated key genes regulating de novo fatty acid synthesis and downregulated genes encoding key rate-limiting enzymes of fatty acid β-oxidation, thereby promoting lipid synthesis and reducing fatty acid oxidation. Generally, our results reveal that B. licheniformis FA6 promotes lipid accumulation in zebrafish through improving lipid synthesis and reducing β-oxidation.

The evolution of very large body size requires a ubiquitous and abundant source of food. In marine environments, the largest animals such as whale sharks are secondary consumers that filter feed on nekton, which is plentiful, although patchy. Consequently, feeding in coastal environments requires cost-efficient foraging that focuses on oceanographic features that aggregate both nektonic prey and marine debris such as floating macroalgae. Consumption of this algae could present an energetic challenge for these animals, unless some component can be digested. Here, we use a multi-technique approach involving amino acid compound-specific stable isotope analysis (CSIA) and fatty acid analysis to determine the trophic level of whale sharks and to identify likely items in the diet. CSIA analyses showed that the species has a trophic level consistent with omnivory. Fatty acid profiles of whale shark tissues, feces and potential prey items suggest that the floating macroalgae, Sargassum, and its associated epibionts is a significant source of food. Although this overcomes the energetic challenge of consumption of floating algae, this mode of feeding and the need to focus on oceanographic features that aggregate prey also increases the threat to the species posed by pollutants such as plastic., (© 2022 Commonwealth of Australia. Ecology © 2022 The Ecological Society of America.)

In degraded coral reef ecosystems, allelopathic macroalgae have received increasing attention from marine ecologists because their secondary metabolites (also known as allelochemicals) kill corals that grow adjacent to them and weaken the recovery of degraded reefs. One well-known coral-killing macroalga is the calcareous red seaweed Galaxaura . However, our knowledge of how coral reef fishes interact with allelopathic algae like Galaxaura is very limited. Here, we documented novel observations of feeding interactions of 17 species of coral reef fishes (herbivorous and carnivorous) with the filamentous Galaxaura divaricata on degraded lagoon patch reefs in Dongsha Atoll (South China Sea). Video analyses showed that territorial farming damselfishes (i.e., Dischistodus perspicillatus , D. prosopotaenia , Hemiglyphidodon plagiometopon , Pomacentrus grammorhynchus , P. adelus , and Neoglyphidodon nigroris ) and juvenile parrotfishes ( Scarus schlegeli , S. ghobban , S. rivulatus , and Chlorurus spilurus ) likely used G. divaricata as a feeding substratum. Further, microscopic analyses revealed that the filamentous surface of G. divaricata harbored a wealth of epiphytic microalgae, such as filamentous cyanobacteria (i.e., Leptolyngbya , Lyngbya , Rivularia , Oscillatoria , and Stigonema ), diatoms (i.e., Synedra , Nitzschia , Mastogloia , and Pleurosigma ), and filamentous red algae (i.e., Heterosiphonia ), suggesting that these fishes targeted the nutrient-rich microscopic epiphytes rather than the nutrient-poor host. Juvenile benthic carnivores (i.e., Labridae, Parupeneus multifasciatus , and Meiacanthus grammistes ) form feeding assemblages with roving parrotfishes to feed on small invertebrates (i.e., amphipods, copepods, isopods, gastropods, and polychaetes) associated with G. divaricata . Given that coral reef fishes appear to target the epiphytes associated with Galaxaura rather than the alga itself, these observations thus substantiate the threat posed by the overgrowth of G. divaricata to coral recovery in degraded reef systems due to the lack of natural grazers., Competing Interests: The authors have declared that no competing interests exist., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Symbiotic gut microbiota in the herbivorous marine fish Kyphosus sydneyanus play an important role in digestion by converting refractory algal carbohydrate into short-chain fatty acids. Here we characterised community composition using both 16S rRNA gene amplicon sequencing and shotgun-metagenome sequencing. Sequencing was carried out on lumen and mucosa samples (radial sections) from three axial sections taken from the hindgut of wild-caught fish. Both lumen and mucosa communities displayed distinct distributions along the hindgut, likely an effect of the differing selection pressures within these hindgut locations, as well as considerable variation among individual fish. In contrast, metagenomic sequences displayed a high level of functional similarity between individual fish and gut sections in the relative abundance of genes (based on sequencing depth) that encoded enzymes involved in algal-derived substrate degradation. These results suggest that the host gut environment selects for functional capacity in symbionts rather than taxonomic identity. Functional annotation of the enzymes encoded by the gut microbiota was carried out to infer the metabolic pathways used by the gut microbiota for the degradation of important dietary substrates: mannitol, alginate, laminarin, fucoidan and galactan (e.g. agar and carrageenan). This work provides the first evidence of the genomic potential of K. sydneyanus hindgut microbiota to convert highly refractory algal carbohydrates into metabolically useful short-chain fatty acids., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Abalone around the world are subject to increasing frequency of marine heatwaves, yet we have a limited understanding of how acute high temperature events impact the physiology of these commercially and ecologically important species. This study examines the impact of a 5 °C temperature increase over ambient conditions for six weeks on the metabolic rates, digestive enzyme activities in the digestive gland, and digestive efficiency of Red Abalone (Haliotis rufescens) and Pāua (H. iris) on their natural diets. We test the hypothesis that abalone digestive function can keep pace with this increased metabolic demand in two separate experiments, one for each species. H. iris had higher food intake in the heat treatment. Both species had higher metabolic rates in the heat treatment with Q 10  = 1.73 and Q 10  = 2.46 for H. rufescens and H. iris, respectively. Apparent organic matter digestibility, protein digestibility, and carbohydrate digestibility did not differ between the heat treatment and the ambient (control) treatment in either experiment. H. rufescens exhibited higher maltase, alanine-aminopeptidase, and leucine-aminopeptidase activities in the heat treatment. Amylase, β-glucosidase, trypsin, and alkaline phosphatase activities in the digestive gland tissue did not differ between temperature treatments. H. iris exhibited lower amylase and β-glucosidase activities in the heat treatment, while maltase, trypsin, leucine-aminopeptidase, and alkaline phosphatase activities did not differ between treatments. We conclude that over six weeks of moderate heat stress both abalone species were able to maintain digestive function, but achieved this maintenance in species-specific ways., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

A Gram-stain-positive, non-spore-forming, rod-shaped, obligately anaerobic bacterium, designated strain BP52G T , was isolated from the hindgut of a Silver Drummer ( Kyphosus sydneyanus ) fish collected from the Hauraki Gulf, New Zealand. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate belonged to the family Erysipelotrichaceae in the phylum Firmicutes and was most closely related to Clostridium saccharogumia with 93.3 % sequence identity. Isolate BP52G T grew on agar medium containing mannitol as the sole carbon source. White, opaque and shiny colonies of the isolate measuring approximately 1 mm diameter grew within a week at 20-28 °C (optimum, 24 °C) and pH 6.9-8.5 (optimum, pH 7.8). BP52G T tolerated the addition of up to 1 % NaCl to the medium. Formate and acetate were the major fermentation products. The major cellular fatty acids were C 16 : 0 , C 16:1n-7t and C 18:1n-7t . The genome sequence of the isolate was determined. Its G+C content was 30.7 mol%, and the 72.65 % average nucleotide identity of the BP52G T genome to its closest neighbour with a completely sequenced genome ( Erysipelatoclostridium ramosum JCM 1298 T ) indicated low genomic relatedness. Based on the phenotypic and taxonomic characteristics observed in this study, a novel genus and species Tannockella kyphosi gen. nov., sp. nov. is proposed for isolate BP52G T (=NZRM 4757 T =JCM 34692 T ).

Many marine herbivorous fishes harbour diverse microbial communities in the hindgut that can play important roles in host health and nutrition. Kyphosus sydneyanus is a temperate marine herbivorous fish that feeds predominantly on brown seaweeds. We employed 16S rRNA gene amplicon sequencing and gas chromatography to characterize microbial communities and their metabolites in different hindgut regions of six K. sydneyanus. Measurements were confined to three distal sections of the intestine, labelled III, IV and V from anterior to posterior. A total of 625 operational taxonomic units from 20 phyla and 123 genera were obtained. Bacteroidota, Firmicutes and Proteobacteria were the major phyla in mean relative abundance, which varied along the gut. Firmicutes (76%) was the most dominant group in section III, whereas Bacteroidota (69.3%) dominated section V. Total short-chain fatty acid (SCFA) concentration was highest in sections IV and V, confirming active fermentation in these two most distal sections. The abundance of Bacteroidota correlated with propionate concentration in section V, while Firmicutes positively correlated with formate in sections III and IV. Acetate levels were highest in sections IV and V, which correlated with abundance of Bacteroidota. Despite differences in gut microbial community composition, SCFA profiles were consistent between individual fish in the different hindgut regions of K. sydneyanus, although proportions of SCFAs differed among gut sections. These findings demonstrate functional compartmentalization of the hindgut microbial community, highlighting the need for regional sampling when interpreting overall microbiome function. These results support previous work suggesting that hindgut microbiota in marine herbivorous fish are important to nutrition in some host species by converting dietary carbohydrates into metabolically useful SCFAs., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

While alimentary tract anatomy in many terrestrial herbivorous vertebrates is well documented, the digestive systems of marine herbivorous fishes are poorly characterised. The gastrointestinal tract (GIT) of four species of marine herbivorous fishes from northeastern New Zealand, butterfish Odax pullus (Labridae), marblefish Aplodactylus arctidens (Aplodactylidae), notch-head marblefish A. etheridgii (Aplodactylidae) and silver drummer Kyphosus sydneyanus (Kyphosidae), were examined using histology and transmission electron microscopy (TEM) to provide a detailed histological and ultrastructural description of gut anatomy. Gastric glands were distributed over rugae in the stomach of A. arctidens, A. etheridgii and K. sydneyanus. The luminal surface of the stomach of these three species was lined by columnar mucous cells, and oxynticopeptic cells lined the glands in the stomach. Villi were present along the length of the intestine in all four species. The anterior intestine had thin musculature, and was lined by absorptive cells with long microvilli and numerous small vesicles in the apical cytoplasm. The posterior intestine was lined by absorptive columnar cells with long microvilli, invaginations between microvilli with electron-dense membranes, and pinocytotic vesicles. Surface area generally decreased from the anterior to posterior intestine. Histological and ultrastructural results were consistent with lipid absorption occurring in the anterior GIT and protein absorption in the posterior GIT. The results of this study indicate clear differences in GIT structure among the study species, and digestion models based on chemical reactor theory were developed to characterise these differences., (© 2021 Wiley Periodicals LLC.)

A new endemic species of triplefin Ruanoho scurra is described from deep water (108216 m) on the shelf region around coastal New Zealand (Northland to Stewart Island). It is differentiated from its congeners by the combination of fresh colour (bright yellow spots on the head and anterior body, oblique lines on the dorsal and anal fins, and sub-vertical lines on the caudal) as well as some proportional measurements. Comments are made on the relationship with its congeners, and evolutionary history of the family in New Zealand waters, along with observations on the habitat in which this new species is found. This paper formally describes the species first mentioned in Stewart Clements 2015:1523 as the polkadot triplefin.

Nibblers (family Girellidae) are reef fishes that are mostly distributed in the Indo-Pacific, with one exception: Girella stuebeli, which is found in the Cabo Verde Archipelago, in the Atlantic Ocean. We capitalized on this unusual distribution to study the evolutionary history of the girellids, and determine the relationship between G. stuebeli and the remaining nibbler taxa. Based on thousands of genomic markers (RAD sequences), we identified the closest relatives of G. stuebeli as being a clade of three species endemic to the northwestern Pacific, restricted to the Sea of Japan and vicinity. This clade diverged from G. stuebeli approximately 2.2 Mya. Two alternative potential routes of migration may explain this affinity: a western route, from the Tropical Eastern Pacific and the Tropical Western Atlantic, and an eastern route via the Indian Ocean and Southern Africa. The geological history and oceanography of the regions combined with molecular data presented here, suggest that the eastern route of invasion (via the Indian Ocean and Southern Africa) is a more likely scenario., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Biological feedbacks generated through patterns of disturbance are vital for sustaining ecosystem states. Recent ocean warming and thermal anomalies have caused pantropical episodes of coral bleaching, which has led to widespread coral mortality and a range of subsequent effects on coral reef communities. Although the response of many reef-associated fishes to major disturbance events on coral reefs is negative (e.g., reduced abundance and condition), parrotfishes show strong feedbacks after disturbance to living reef structure manifesting as increases in abundance. However, the mechanisms underlying this response are poorly understood. Using biochronological reconstructions of annual otolith (ear stone) growth from two ocean basins, we tested whether parrotfish growth was enhanced following bleaching-related coral mortality, thus providing an organismal mechanism for demographic changes in populations. Both major feeding guilds of parrotfishes (scrapers and excavators) exhibited enhanced growth of individuals after bleaching that was decoupled from expected thermal performance, a pattern that was not evident in other reef fish taxa from the same environment. These results provide evidence for a more nuanced ecological feedback system-one where disturbance plays a key role in mediating parrotfish-benthos interactions. By influencing the biology of assemblages, disturbance can thereby stimulate change in parrotfish grazing intensity and ultimately reef geomorphology over time. This feedback cycle operated historically at within-reef scales; however, our results demonstrate that the scale, magnitude, and severity of recent thermal events are entraining the biological responses of disparate communities to respond in synchrony. This may fundamentally alter feedbacks in the relationships between parrotfishes and reef systems., (© 2019 John Wiley & Sons Ltd.)

Epulopiscium sp. type B (Lachnospiraceae) is an exceptionally large, highly polyploid, intestinal symbiont of the coral reef dwelling surgeonfish Naso tonganus. These obligate anaerobes do not form mature endospores and reproduce solely through the production of multiple intracellular offspring. This likely makes them dependent on immediate transfer to a receptive host for dispersal. During reproduction, only a small proportion of Epulopiscium mother-cell DNA is inherited. To explore the impact of this unusual viviparous lifestyle on symbiont population dynamics, we investigated Epulopiscium sp. type B and their fish hosts collected over the course of two decades, at island and reef habitats near Lizard Island, Australia. Using multi-locus sequence analysis, we found that recombination plays an important role in maintaining diversity of these symbionts and yet populations exhibit linkage disequilibrium (LD). Symbiont populations showed spatial but not temporal partitioning. Surgeonfish are long-lived and capable of traveling long distances, yet the population structures of Epulopiscium suggest that adult fish tend to not roam beyond a limited locale. Codiversification analyses and traits of this partnership suggest that while symbionts are obligately dependent on their host, the host has a facultative association with Epulopiscium. We suggest that congression of unlinked markers contributes to LD estimates in this and other recombinant populations of bacteria. The findings here inform our understanding of evolutionary processes within intestinal Lachnospiraceae populations.

The present study describes the age and growth of the leatherjacket Meuschenia scaber, a common Australasian monacanthid and valued by-catch of the inshore bottom trawl fishery in New Zealand. Age was determined from the sagittal otoliths of 651 individuals collected between July 2014 and March 2016 in the Hauraki Gulf of New Zealand. Otolith sections revealed alternating opaque and translucent zones and edge-type analysis demonstrated that these are deposited annually. Meuschenia scaber displayed rapid initial growth, with both males and females reaching maturity in 1-2 years and 50% of both sexes matured at 1·5 years. Maximum age differed substantially between the sexes, at 9·8 years for males and 17·1 years for females. Growth rate was similar between sexes, although males reached greater mass at age than females in the early part of the lifespan. The length-mass relationship differed significantly between the sexes, with males displaying negative allometric growth and females isometric growth. Female condition was highest in July, declined in August with the onset of spawning and showed a slight peak in January and February, immediately following the spawning season. This study substantially extends the maximum longevity recorded for monacanthids, although males had much shorter lifespans and higher mortality, than females., (© 2018 The Fisheries Society of the British Isles.)

Sea chubs of the family Kyphosidae are major consumers of macroalgae on both temperate and tropical reefs, where they can comprise a significant proportion of fish biomass. However, the relationships and taxonomic status of sea chubs (including the junior synonyms Hermosilla, Kyphosus, Neoscorpis and Sectator) worldwide have long been problematical due to perceived lack of character differentiation, complicating ecological assessment. More recently, the situation has been further complicated by publication of conflicting taxonomic treatments. Here, we resolve the relationships, taxonomy and distribution of all known species of sea chubs through a combined analysis of partial fragments from mitochondrial markers (12s, 16s, cytb, tRNA -Pro, -Phe, -Thr and -Val) and three nuclear markers (rag1, rag2, tmo4c4). These new results provide independent evidence for the presence of several junior synonyms among Atlantic and Indo-Pacific taxa, demonstrating that several sea chub species are more widespread than previously thought. In particular, our results can reject the hypothesis of endemic species in the Atlantic Ocean. At a higher taxonomic level, our results shed light on the relationships between Girellidae, Kuhliidae, Kyphosidae, Microcanthidae, Oplegnathidae and Scorpididae, with Scorpididae resolved as the sister group to Kyphosidae., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Input data files for inferring the relationship among the family Kyphosidae, as presented in (Knudsen and Clements, 2016) [1], is here provided together with resulting topologies, to allow the reader to explore the topologies in detail. The input data files comprise seven nexus-files with sequence alignments of mtDNA and nDNA markers for performing Bayesian analysis. A matrix of recoded character states inferred from the morphology examined in museum specimens representing Dichistiidae, Girellidae, Kyphosidae, Microcanthidae and Scorpididae, is also provided, and can be used for performing a parsimonious analysis to infer the relationship among these perciform families. The nucleotide input data files comprise both multiple and single representatives of the various species to allow for inference of the relationship among the species in Kyphosidae and between the families closely related to Kyphosidae. The '.xml'-files with various constrained relationships among the families potentially closely related to Kyphosidae are also provided to allow the reader to rerun and explore the results from the stepping-stone analysis. The resulting topologies are supplied in newick-file formats together with input data files for Bayesian analysis, together with '.xml'-files. Re-running the input data files in the appropriate software, will enable the reader to examine log-files and tree-files themselves.

In ectotherms, growth rate, body size and maturation rate covary with temperature, with the direction and magnitude of variation predicted by the Temperature-Size Rule (TSR). Nutritional quality or availability of food, however, may vary over latitudinal gradients, resulting in ambiguous effects on body size and maturation rate. The Temperature-Constraint Hypothesis (TCH) predicts that marine herbivorous ectotherms are nutritionally compromised at latitudes exceeding 30°. This provides an opportunity to resolve the contrasting demographic responses of ectotherms to variation in temperature and nutritional status over latitudinal gradients. This study uses analysis of demographic rates to evaluate the predictions of the TSR in a marine herbivorous ectotherm sampled over a significant latitudinal gradient. The direction and magnitude of demographic variation was established in the marine herbivorous fish, Odax pullus (the butterfish), and compared with that of a phylogenetically related but trophically distinct species, the carnivorous Notolabrus fucicola (the banded wrasse). Both species were sampled at three locations across the length of New Zealand covering latitudes between 35°S and 49°S. Growth rate, mean size-at-age, age- and size-at-maturity, life span and abundance were estimated for each species at each location. Demographic traits of both taxa varied with latitude. Both species showed slower initial growth rates, and matured later at a larger body size at higher latitudes than populations sampled at lower latitudes. In addition, abundances increased significantly at higher latitudes in both species. These results were consistent with the TSR but not with the TCH, confirming that nutritional ecology (herbivore vs. carnivory) did not determine demographic patterns over a biologically significant latitudinal gradient. Results from this study suggest that the absence of herbivorous reef fishes from the higher latitudes of the Northern Hemisphere may not reflect a general physiological mechanism as suggested by the TCH and highlights the need to clarify the evolutionary histories of the marine biota of each hemisphere., (© 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.)

High-throughput sequencing approaches have enabled characterizations of the community composition of numerous gut microbial communities, which in turn has enhanced interest in their diversity and functional relationships in different groups of vertebrates. Although fishes represent the greatest taxonomic and ecological diversity of vertebrates, our understanding of their gut microbiota and its functional significance has lagged well behind that of terrestrial vertebrates. In order to highlight emerging issues, we provide an overview of research on fish gut microbiotas and the biology of their hosts. We conclude that microbial community composition must be viewed within an informed context of host ecology and physiology, and that this is of particular importance with respect to research planning and sampling design., (© 2014 John Wiley & Sons Ltd.)

A molecular phylogenetic analysis with complete species sampling of the family Kyphosidae revealed several discrepancies with the current taxonomy. We thus undertook a complete taxonomic revision of all kyphosid genera, i.e. Kyphosus Lacepède, 1801, and the monotypic Hermosilla Jenkins and Evermann, 1889, Sectator Jordan and Evermann, 1903 and Neoscorpis Smith, 1931. Species delimitation was determined on the basis of congruence between (a) monophyletic groupings in the molecular phylogeny, and (b) clusters of morphological variation in type material. Twelve species are supported and redescribed. Both Hermosilla and Sectator are considered junior synonyms of Kyphosus. Kyphosus azureus (Jenkins & Evermann, 1889) and K. ocyurus (Jordan & Gilbert, 1882) are redescribed accordingly. We designate a neotype for Kyphosus cornelii (Whitley, 1944), as the original material is lost, and new material was collected at the type locality for this study to facilitate comparison with other species of Kyphosus. Kyphosus sandwicensis (sensu Sauvage, 1880) was found to be a junior synonym of K. elegans (Peters, 1869). Kyphosus incisor (Cuvier in Cuvier & Valenciennes, 1831) and K. analogus (Gill, 1862) are considered junior synonyms of K. vaigiensis (Quoy & Gaimard, 1825). Kyphosus gallveii (Cunningham, 1910), K. pacificus Sakai and Nakabo, 2004 and K. lutescens (Jordan & Gilbert, 1882) are all considered junior synonyms of K. sectatrix (Linnaeus, 1758). One of the two syntype specimens of K. sectatrix was identified as the holotype of Pimelepterus bosquii (Lacepède, 1802), and proved to be a specimen of K. bigibbus Lacepède, 1801. This specimen is re-assigned as a non-type of K. bigibbus. Full re-descriptions of the following valid species are presented: K. bigibbus, K. cinerascens (Forsskål, 1775), K. cornelii, K. elegans, K. hawaiiensis Sakai and Nakabo, 2004, K. gladius Knudsen and Clements, 2013, K. sydneyanus (Günther, 1886) and K. vaigiensis, together with a key to the family. The distribution of Kyphosus species is reconsidered based on our taxonomic revision, indicating that four species (K. bigibbus, K. cinerascens, K. sectatrix and K. vaigiensis) occur in both the Atlantic and Indo-Pacific regions.

Two morphologically distinct forms of the nominal species Kyphosus sydneyanus (Günther, 1886) (Kyphosidae) were discerned while collecting off Western Australia near Perth in 2009. A morphological comparison with recognized species of Kyphosus and an analysis of mtDNA (Cytochrome b, control region, 12S and 16S) and three nDNA markers (RAG1, RAG2 and Tmo-4C4) demonstrated that the more elongate of these forms was an undescribed species of Kyphosus. It differs from congeners in the Pacific and Indian Oceans in the combination of the following characters: green bar on the operculum, 11-12 dorsal soft fin rays, depth of caudal peduncle 9.9-11.8 % SL, body depth 33.3-41.6 % SL, 55-63 scales in lateral line, 12-16 interorbital scales, 44-55 pored scales in the lateral line, 3-5 gill rakers on upper limb of first gill arch internally, 11-15 gill rakers on lower limb of first gill arch internally, 15-19 total gill rakers on first gill arch, and by having 10 precaudal vertebrae and 16 caudal vertebrae. Examination of museum specimens and available underwater photographs suggests that the new species is restricted to Western Australia, and to date it has been recorded between the Houtman Abrolhos Islands and Albany. Discrepancies between the type specimen and original description of Segutilum klunzingeri Whitley made it impossible to determine the relationship between this taxon and the new species from Western Australia, and thus we consider S. klunzingeri a nomen dubium.

Two isolates of the pycnotrichid ciliate genus, Vestibulongum, were collected from the host fish, Acanthurus xanthopterus, from two locations in the Southern Pacific Ocean. One was from the Great Barrier Reef (GBR), and a second from Papua New Guinea. These sites are thousands of km from the type locality, off the coast of South Africa. New data were collected from protargol-stained samples to more fully characterize the general form and light microscopic structures of the ciliate. Specimens from all three sites had a long vestibule, characteristic of most members of the family. Data suggest that specimens from each site are the same genus. The kinetids of the Vestibulongum isolated from the GBR contained the typical components of postciliary, transverse, and nemodesmatal microtubules, and Kd fibrils. Also, two quite different forms of endomacronuclear bacteria were observed and are described. One of those has distinct endospores, which are similar to endospores in nuclear endosymbiotic bacteria in a species of Balantidium from the gut of another species of surgeonfish., (© 2012 The Author(s) Journal of Eukaryotic Microbiology © 2012 International Society of Protistologists.)

Background: Epulopiscium sp. type B, a large intestinal bacterial symbiont of the surgeonfish Naso tonganus, does not reproduce by binary fission. Instead, it forms multiple intracellular offspring using a process with morphological features similar to the survival strategy of endospore formation in other Firmicutes. We hypothesize that intracellular offspring formation in Epulopiscium evolved from endospore formation and these two developmental programs share molecular mechanisms that are responsible for the observed morphological similarities., Results: To test this, we sequenced the genome of Epulopiscium sp. type B to draft quality. Comparative analysis with the complete genome of its close, endospore-forming relative, Cellulosilyticum lentocellum, identified homologs of well-known sporulation genes characterized in Bacillus subtilis. Of the 147 highly conserved B. subtilis sporulation genes used in this analysis, we found 57 homologs in the Epulopiscium genome and 87 homologs in the C. lentocellum genome., Conclusions: Genes coding for components of the central regulatory network which govern the expression of forespore and mother-cell-specific sporulation genes and the machinery used for engulfment appear best conserved. Low conservation of genes expressed late in endospore formation, particularly those that confer resistance properties and encode germinant receptors, suggest that Epulopiscium has lost the ability to form a mature spore. Our findings provide a framework for understanding the evolution of a novel form of cellular reproduction.

Parrotfishes and surgeonfishes perform important functional roles in the dynamics of coral reef systems. This is a consequence of their varied feeding behaviors ranging from targeted consumption of living plant material (primarily surgeonfishes) to feeding on detrital aggregates that are either scraped from the reef surface or excavated from the deeper reef substratum (primarily parrotfishes). Increased fishing pressure and widespread habitat destruction have led to population declines for several species of these two groups. Species-specific data on global distribution, population status, life history characteristics, and major threats were compiled for each of the 179 known species of parrotfishes and surgeonfishes to determine the likelihood of extinction of each species under the Categories and Criteria of the IUCN Red List of Threatened Species. Due in part to the extensive distributions of most species and the life history traits exhibited in these two families, only three (1.7%) of the species are listed at an elevated risk of global extinction. The majority of the parrotfishes and surgeonfishes (86%) are listed as Least Concern, 10% are listed as Data Deficient and 1% are listed as Near Threatened. The risk of localized extinction, however, is higher in some areas, particularly in the Coral Triangle region. The relatively low proportion of species globally listed in threatened Categories is highly encouraging, and some conservation successes are attributed to concentrated conservation efforts. However, with the growing realization of man's profound impact on the planet, conservation actions such as improved marine reserve networks, more stringent fishing regulations, and continued monitoring of the population status at the species and community levels are imperative for the prevention of species loss in these groups of important and iconic coral reef fishes.

Epulopiscium sp. type B is an enormous intestinal symbiont of the surgeonfish Naso tonganus. Intracellular offspring production in Epulopiscium shares features with endospore formation. Here, we characterize the spoIIE homolog in Epulopiscium. The timing of spoIIE gene expression and presence of interacting partners suggest that the activation of σ(F) occurs early in Epulopiscium offspring development.

The sexual ontogeny of butterfish Odax pullus was examined in the Hauraki Gulf of New Zealand through histological analysis of gonad material, size and age information and seasonal patterns of sexual maturation. The patterns of gonad development and schedules of male recruitment were established and sexual ontogeny of O. pullus was diagnosed as monandric protogyny, with all males developing from mature females after female-to-male sex reversal. All individuals underwent an immature female phase before maturing as functional females at 228·7-264·8 mm fork length (L(F) ) and at 1·1-1·5 years of age, and there was no evidence of a juvenile bisexual phase. Degenerating mature oogenic elements were found in the gonad lumen of individuals with developing spermatogenic tissue, providing histological evidence for functional protogyny. Sex change was estimated to occur at 359-379 mm L(F) and 2-3 years of age. The diagnosis of monandric protogyny for O. pullus coincided with the pattern of sexual ontogeny seen in the majority of labrids, particularly those of the same clade (tribe Hypsigenyini) and contrasted with that seen in a number of other temperate labrids. This study suggests that the protogynous mode of sexual development in O. pullus is likely to be lineage-specific, i.e. associated with the phylogeny of labrid sexual development, and is not constrained by environmental effects on the evolution of sex change in temperate regions., (© 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.)

The heart is acutely sensitive to temperature in aquatic ectotherms and appears to fail before any other organ as the thermal maximum is reached, although the exact cause of this failure remains unknown. The heart is highly aerobic and therefore dependent on mitochondrial oxidative phosphorylation (OXPHOS) to meet energy requirements, but the role of cardiac mitochondria in limiting heart function at high temperatures remains unclear. We used permeabilised ventricle fibres to explore heart mitochondrial function in situ in three closely related species of small New Zealand triplefin fishes in response to temperature. We compared this to measures of whole animal respiration rates and critical oxygen tensions in these fishes. Bellapiscis medius, an intertidal species, had the greatest tolerance to hypoxia at higher temperatures and had more efficient OXPHOS at 30°C than the two subtidal species Forsterygion varium and F. malcolmi. B. medius also displayed the highest cytochrome c oxidase flux, which may in part explain how B. medius tolerates higher temperatures and hypoxia. Triplefin heart mitochondria exhibit decreased coupling to phosphorylation with increasing temperature. This most likely impairs ATP supply to the heart at elevated temperatures, potentially contributing to heart failure at ecologically relevant temperatures.

The mechanoreceptive lateral line system in fishes detects hydrodynamic stimuli and plays a critical role in many fundamental behaviours, including orientation to water currents and the detection of stationary objects, prey and predators. Interspecific variation in lateral line structure may result from a process of functional adaptation, with the background level of hydrodynamic activity proposed as an important selective pressure. Here we use the eight species of the ecologically diverse New Zealand marine triplefin fish of the genus Forsterygion and one species from the sister genus Notoclinops to investigate interspecific differences in lateral line morphology and to assess the relationship between lateral line characteristics and exposure to wave energy (fetch/depth ratio). Overall, the results show that lateral line traits are divergent between species, and these differences could in part be related to the wave exposure of the habitats that the species occupy. Specifically, numbers of canal neuromasts differed significantly between species, and most canal groupings increased in neuromast number with fetch/depth ratio, while the number and area of some superficial neuromast groupings decreased significantly with exposure. Distribution of superficial neuromasts along the trunk in the semi-pelagic and paedomorphic species F. maryannae differed from the other, demersal species, which may be associated with the unique lifestyle of this species and/or developmental processes. Canal architecture also differed considerably between species, but displayed no relationship with fetch/depth ratio. The results from this study indicate that some interspecific differences in lateral line organs may be a by-product of selection for habitat divergence. Future work should explore additional causal factors that might have influenced the evolution of lateral morphology in these species, including phylogenetic and allometric effects., (Copyright 2010 S. Karger AG, Basel.)

Triplefin fishes (Family Tripterygiidae) dominate the New Zealand temperate coastal fish fauna in diversity (26 endemic species, 14 genera). Most species appear to have evolved as a local radiation and mostly occupy sympatric distributions throughout New Zealand. To investigate the forces driving current gene-flow patterns and past evolutionary histories, we searched for common patterns of population genetic subdivision within eight species sampled throughout their distributions [mitchochondrial DNA (mtDNA) control region, n = 1086]. We hypothesised that common phylogeographical and population differentiation patterns would reveal past or ongoing physical processes, with differences reflecting stochastic or species-specific processes. Striking differences between species were apparent, with strong phylogeographical structure detected in Grahamina capito and the estuarine species G. nigripenne. G. capito fell into three distinct geographically restricted lineages. G. nigripenne largely separated into northern and southern lineages (Phi(ST) 0.834). Strong population structuring and isolation by distance was evident in Bellapiscis medius, B. lesleyae and Forsterygion lapillum (Phi(ST) 0.686, 0.436 and 0.115, respectively). High gene flow was apparent in G. gymnota and Ruanoho whero, and F. varium. However, for the latter species, isolation was apparent with samples collected from the offshore Three Kings Islands. Overall, a strong relationship was found between habitat depth and population structure among species, and species inhabiting shallower water habitats showed lower genetic diversity with higher levels of population subdivision. High-latitude populations generally showed low haplotype and nucleotide diversity. These data suggest that processes resulting from intraspecific differences in habitat preference, climatic histories and/or larval ecologies have subdivided populations of shallow water triplefin species.

Epulopiscium sp. type B, a member of the Firmicutes, is a large (up to 300 microm), cigar-shaped bacterial symbiont of surgeonfish that propagates itself by forming multiple intracellular offspring. This unusual form of reproduction is an apparent modification of a developmental program used by some Firmicutes to produce an endospore. At the onset of offspring formation, the Epulopiscium cell divides at both poles. The polar cells are engulfed by the larger mother cell and grow within the mother cell. At the final stages of development, the Epulopiscium mother cell lyses. Here we describe changes in Epulopiscium cell structure, focusing on mother cell DNA replication and cell death. DNA replication was examined by labeling cells with the nucleotide analog bromodeoxyuridine. As expected, DNA replication occurs in the developing offspring. However, well after passage of genetic information from parent to offspring is complete, DNA within the mother cell continues to replicate. Using fluorescence microscopy, we found that near the end of the offspring growth cycle, mother cell DNA disintegrates. The mother cell membrane and wall deteriorate as well. DNA replication within this terminally differentiated cell indicates the importance of mother cell nucleoids in cell maintenance and the development of offspring. The synchronized timing of mother cell deterioration within a population suggests that the Epulopiscium mother cell undergoes a programmed cell death. The programmed death of the mother cell may allow for the timely release of resources accumulated in the mother cell to provide nutrients to populations of these intestinal microbes and their host.

Cells rely on diffusion to move metabolites and biomolecules. Diffusion is highly efficient but only over short distances. Although eukaryotic cells have broken free of diffusion-dictated constraints on cell size, most bacteria and archaea are forced to remain small. Exceptions to this rule are found among the bacterial symbionts of surgeonfish; Epulopiscium spp. are cigar-shaped cells that reach lengths in excess of 600 mum. A large Epulopiscium contains thousands of times more DNA than a bacterium such as Escherichia coli, but the composition of this DNA is not well understood. Here, we present evidence that Epulopiscium contains tens of thousands of copies of its genome. Using quantitative, single-cell PCR assays targeting single-copy genes, we have determined that copy number is positively correlated with Epulopiscium cell size. Although other bacteria are known to possess multiple genomes, polyploidy of the magnitude observed in Epulopiscium is unprecedented. The arrangement of genomes around the cell periphery may permit regional responses to local stimuli, thus allowing Epulopiscium to maintain its unusually large size. Surveys of the sequences of single-copy genes (dnaA, recA, and ftsZ) revealed genetic homogeneity within a cell consistent with only a small amount ( approximately 1%) of the parental DNA being transferred to the next generation. The results also suggest that the abundance of genome copies in Epulopiscium may allow for an unstable genetic feature, a long mononucleotide tract, in an essential gene. With the evolution of extreme polyploidy and large cell size, Epulopiscium has acquired some of the advantages of eukaryotic cells.

Enzymatic degradation of algal carbohydrates was examined in the New Zealand herbivorous fishes Parma alboscapularis (Pomacentridae), Aplodactylus etheridgii (Aplodactylidae), Girella tricuspidata and G. cyanea (Girellidae). Enzyme extract taken from the anterior gut wall, gut fluid and microbial pellet from sections sampled along the gut were tested for activity against starch, carrageenan, agarose and carboxymethylcellulose. Hydrolysis of starch was greater than for all other substrates tested. Endogenous (host-produced) activity in the anterior gut fluid varied between species in the order G. tricuspidata (7700 units mL(-1))>G. cyanea (2300 units mL(-1))>P. alboscapularis (2000)>A. etheridgii (1400 units mL(-1)) where one unit is equivalent to 1 mug of reducing sugar released per minute. Activity decreased markedly along the gut in all cases, so that at the posterior end of the gut only 0.3-8% of the anterior activity remained in the gut fluid. Enzyme activity against structural carbohydrates was lower than that against starch, and was of exogenous (produced by resident microbiota) origin in all species although the location of activity along the gut differed. The microbial extract of A. etheridgii displayed the highest activity against carrageenan and agarose in all gut sections, reaching maxima of 47 units mL(-1) against carrageenan and 35 units mL(-1) against agarose in the mid-gut microbial extract. Carrageenase and agarase activity in the other three species was <10 units mL(-1) for all gut sections. Results suggest that carrageenan and agarose are potentially important substrates for microbial fermentation, particularly in A. etheridgii, and that there is microbial activity in the mid-gut of this species, rather than primarily in the hind-gut as in other herbivorous species.

The genome sizes of 18 species of New Zealand triplefin fishes (family Tripterygiidae) were determined by flow cytometry of erythrocytes. The evolutionary relationships of these species were examined with a molecular phylogeny derived from DNA sequence data based on 1771 base pairs from fragments of three mitochondrial loci (12S and 16S ribosomal RNA, and the control region) and one nuclear locus (ETS2). Haploid genome sizes ranged from .85 pg (1C) to 1.28 pg with a mean of 1.15 +/- .01pg. Genome size appeared to be highly plastic, with up to 20% variation occurring within genera and a 50% difference in size between the smallest and the largest genome. No evidence was found to indicate polyploidy as a mechanism for speciation in New Zealand triplefins. Factors suggested to influence genome sizes of other organisms, such as morphological complexity, neoteny, and longevity, do not appear to be associated with shifts in the genome sizes of New Zealand triplefins.

The Labridae is one of the most structurally and functionally diversified fish families on coral and rocky reefs around the world, providing a compelling system for examination of evolutionary patterns of functional change. Labrid fishes have evolved a diverse array of skull forms for feeding on prey ranging from molluscs, crustaceans, plankton, detritus, algae, coral and other fishes. The species richness and diversity of feeding ecology in the Labridae make this group a marine analogue to the cichlid fishes. Despite the importance of labrids to coastal reef ecology, we lack evolutionary analysis of feeding biomechanics among labrids. Here, we combine a molecular phylogeny of the Labridae with the biomechanics of skull function to reveal a broad pattern of repeated convergence in labrid feeding systems. Mechanically fast jaw systems have evolved independently at least 14 times from ancestors with forceful jaws. A repeated phylogenetic pattern of functional divergence in local regions of the labrid tree produces an emergent family-wide pattern of global convergence in jaw function. Divergence of close relatives, convergence among higher clades and several unusual 'breakthroughs' in skull function characterize the evolution of functional complexity in one of the most diverse groups of reef fishes.