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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.

The study of digestive physiology provides a framework for analyzing food resources, feeding patterns, and evolutionary trends in vertebrate herbivores. Most of the research in this field, nutritional ecology, has been focused on terrestrial herbivores, especially mammals. By integrating physiological, demographic, and evolutionary approaches, the study of terrestrial herbivores has generated several important hypotheses, notably on factors determining body mass. Marine vertebrate herbivores are abundant and locally diverse, but with the exception of reptiles and mammals, we lack information on digestive physiology and processing of plant foods, the key element in terrestrial studies. This review provides a foundation for a nutritional ecology of marine vertebrate herbivores, especially teleost fish, by summarizing the available information on their digestive physiology and identifying research priorities in the field.

Summary 1.Marine herbivorous fishes are considered to be of critical importance in determining the biological structure of shallow reef environments, and by implication have key roles in carbon flux in reef ecosystems. Despite this, the nutritional processes that underpin these critical ecological roles have received comparatively little attention. 2.Here we give an overview of recent progress in the nutritional ecology of marine herbivorous fishes, and then examine two recent paradigms that we consider important in the development of the field: (i) the role of temperature in latitudinal gradients of diversity and abundance, and (ii) the impact of these fishes on coral reefs. Our aim is to illustrate how an integrative nutritional ecology approach can enrich insights gained from studies of fish herbivory, and to emphasize the distinctive differences between herbivory in marine and terrestrial systems. 3. We argue that much of the work on trophic biology in marine herbivorous fishes has focused on the ecological impacts of fishes on reefs, the deterrent properties of marine algae, and the morphological and mechanical aspects of ingestion. This has come at the expense of two of the elements necessary for an integrative understanding of feeding ecology, that is, food composition and the physiological processes involved in nutrient extraction and utilization. Together, these factors have hindered the development of the nutritional framework for analysing food resources, feeding patterns and evolutionary trends that has proved successful for terrestrial vertebrate herbivores. 4. The reef grazing and algal secondary metabolite paradigms, while both extremely productive, have failed to develop the clear predictive framework for diet choice required in broader contexts such as reef management and understanding the evolution of herbivory. The lack of a focus on nutritional factors has led to premature conclusions on the influence of temperature on algal digestion, both at the level of digestive processes and the biogeography of marine faunas. 5. Some marine herbivorous fishes appear to be bending the 'rules' of hindgut fermentation, especially with respect to temperature and fermentation substrates, and so the study of nutritional ecology in these animals has potential to generate novel insights for the field of vertebrate nutrition in general.

Symbioses with gut microorganisms provides a means by which terrestrial herbivores are able to obtain energy. These microorganisms ferment cell wall materials of plants to short-chain fatty acids (SCFA), which are then absorbed and used by the host animal. Many marine herbivorous fishes contain SCFA (predominantly acetate) in their hindgut, indicative of gut microbial activity, but rates of SCFA production have not been measured. Such information is an important prerequisite to understanding the contribution that gut microorganisms make in satisfying the energy needs of the fish. We have estimated the rates of acetate production in the gut of three species of temperate marine herbivorous fish from northeastern New Zealand: Kyphosus sydneyanus (family Kyphosidae), Odax pullus (family Odacidae), and Aplodactylus arctidens (family Aplodactylidae). Ex vivo preparations of freshly caught fish were maintained with their respiratory and circulatory systems intact, radiolabeled acetate was injected into ligated hindgut sections, and gut fluid was sampled at 20-min intervals for 2 h. Ranges for acetate turnover in the hindguts of the studied species were determined from the slope of plots as the log of the specific radioactivity of acetate versus time and pool size, expressed on a nanomole per milliliter per minute basis. Values were 450 to 570 (K. sydneyanus), 373 to 551 (O. pullus), and 130 to 312 (A. arctidens). These rates are comparable to those found in the guts of herbivorous reptiles and mammals. To determine the contribution of metabolic pathways to the fate of acetate, rates of sulfate reduction and methanogenesis were measured in the fore-, mid-, and hindgut sections of the three fish species. Both rates increased from the distal to proximal end of the hindgut, where sulfate reduction accounted for only a small proportion (<5%) of acetate methyl group transformed to CO 2 , and exceeded methanogenesis from acetate by >50-fold. When gut size was taken into account, acetate uptake from the hindgut of the fish species, determined on a millimole per day per kilogram of body weight basis, was 70 (K. sydneyanus), 18 (O. pullus), and 10 (A. arctidens).Marine herbivorous fish harbor a great diversity of gut microorganisms (1, 9-11, 15, 23, 33, 40, 43, 45). Despite their importance in terms of microbial biodiversity, the role of these microorganisms in the digestive processes of the host fish is not well understood. In contrast, it is well known that most terrestrial vertebrate herbivores contain populations of symbiotic organisms that play a key role in digestion by breaking down plant cell walls (cellulose and hemicellulose) to simple compounds such as short-chain fatty acids (SCFA). The SCFA are then taken up by the host and are used for energy generation and biosynthesis (44).The algae eaten by marine herbivorous fishes are phylogenetically diverse. Unlike terrestrial plants, algae are supported by water and have a lower proportion of structural elements to cell contents (8). Consequently, it is not surprising that ...

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 m. 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 (Ϸ1%) 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.dnaA ͉ Epulopiscium ͉ large bacteria ͉ mononucleotide repeat ͉ polyploid I t is well appreciated that many eukaryotes are orders of magnitude larger than all known members of the Bacterial and Archaeal domains. Eukaryotes have broken free of constraints on cell size by the development of sophisticated nutrient uptake systems, subcellular compartmentalization, and the use of a cytoskeleton and motor proteins to transport vesicles. With the further advance of multicellularity, cell and tissue specialization have allowed eukaryotes to attain tremendous dimensions (1, 2). Until recently (3, 4), bacterial (and archaeal) cells were considered simple, displaying little subcellular organization. Although we now know that bacterial cells are also highly organized, possessing motor and cytoskeletal proteins, and even extensive intracellular membranes in some instances (5), these cells are believed to rely on diffusion to access nutrients and other metabolically important chemicals. Diffusion coefficients of small molecules may impose time constraints on metabolite flux (6) that require bacterial cells to maintain very high surface-tovolume ratios. As a result, no part of the cytoplasm is very far from the external environment, and so exchange is rapid enough to sustain metabolic processes. Most large bacteria fit this paradigm and maintain a very thin cytoplasm; they are extremely long and sle...

LETTERSUndercover. Many Alpheidae shrimps live deep in the reef and are impossible to collect nonlethally. Published by AAAS

Phylogenetic reconstruction of the evolutionary relationships among 61 of the 70 species of the parrotfish genera Chlorurus and Scarus (Family Labridae) based on mitochondrial and nuclear gene sequences retrieved 15 well‐supported clades with mid Pliocene/Pleistocene diversification. Twenty‐two reciprocally monophyletic sister‐species pairs were identified: 64% were allopatric, and the remainder were sympatric. Age of divergence was similar for allopatric and sympatric species pairs. Sympatric sister pairs displayed greater divergence in morphology, ecology, and sexually dimorphic colour patterns than did allopatric pairs, suggesting that both genetic drift in allopatric species pairs and ecologically adaptive divergence between members of sympatric pairs have played a role in diversification. Basal species typically have small geographical ranges and are restricted to geographically and ecologically peripheral reef habitats. We found little evidence that a single dominant process has driven diversification, nor did we detect a pattern of discrete, sequential stages of diversification in relation to habitat, ecology, and reproductive biology. The evolution of Chlorurus and Scarus has been complex, involving a number of speciation processes. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107, 529–557.