Biogeographic and Quantitative Analyses of Abundant Uncultivated γ-Proteobacterial Clades from Marine Sediment

16S rRNA gene-based molecular analyses revealed the presence of several large and so far uncultivated clades within class γ-Proteobacteria, designated γ-proteobacterial marine sediment (GMS) clades 1 to 4, in marine sediment. The GMS clades appear only indigenous to marine sediment and so far have an unknown functionality. SYBR Green–based real-time PCR analyses using GMS clade-specific primers indicated GMS clades were a significant part of the bacterial community (0.3–8.7% of total 16S rRNA genes) in both polar and temperate marine sediment samples. Univariate statistical analyses indicated that GMS clade communities were indistinguishable in two temperate coastal sediment samples even though these possessed very different mean grain sizes, organic contents, and organic loading rates. GMS clade communities were slightly different (p < 0.05) between polar and temperate sites, suggesting that psychrophilic adaptation among GMS clade taxa corresponds only to subtle phylogenetic differences. Similar levels of difference were also observed through a sediment core reflecting that through the sediment core history, which spanned ∼3000 years, GMS clonal diversity shifted only marginally.     

Variable effects of sediment addition on stream benthos

Two upper Piedmont streams were studied to determine the effects of road construction, especially sediment inputs. Benthic macroinvertebrate data suggest that the stream community responded to sediment additions in two different ways. Under high flow conditions the benthic fauna occurs mainly on rocky substrates. As sediment is added to a stream the area of available rock habitat decreases, with a corresponding decrease in benthic density. There is, however, little change in community structure. Under low flow conditions, stable-sand areas may support high densities of certain taxa. Density of the benthic macroinvertebrates in these areas may be much greater than the density recorded in control areas, and there are distinct changes in community structure.     

Phylogenetic study of benthic, spine-bearing prorocentroids, including Prorocentrum fukuyoi sp. nov.

Species of prorocentroid dinoflagellates are common in marine benthic sediment and epibenthic habitats, as well as in planktonic habitats. Marine planktonic prorocentroids typically possess a small spine in the apical region. In this study, we describe a new, potentially widely distributed benthic species of Prorocentrum, P. fukuyoi sp. nov., from tidal sand habitats in several sites in Australia and from central Japan. This species was found to possess an apical spine or flange and was sister species to P. emarginatum. We analyzed the phylogeny of the group including this new species, based on large subunit (LSU) rDNA sequences. The genus contained a high level of divergence in LSU rDNA, in some cases among sister taxa. P. fukuyoi and P. emarginatum were found to be most closely related to a clade of generally planktonic taxa. Several morphological features may constitute more informative synapomorphies than habitat in distinguishing clades of prorocentroid species.     

Ciliates along Oxyclines of Permanently Stratified Marine Water Columns

Studies of microbial communities in areas of the world where permanent marine water column oxyclines exist suggest they are “hotspots” of microbial activity, and that these water features and the anoxic waters below them are inhabited by diverse protist taxa, including ciliates. These communities have minimal taxonomic overlap with those in overlying oxic water columns. Some ciliate taxa have been detected in multiple locations where these stable water column oxyclines exist; however, differences in such factors as hydrochemistry in the habitats that have been studied suggest local selection for distinct communities. We compare published data on ciliate communities from studies of deep marine water column oxyclines in Caricao Basin, Venezuela, and the Black Sea, with data from coastal, shallower oxycline waters in Framvaren and Mariager fjords, and from several deep‐sea hypersaline anoxic basins in the Eastern Mediterranean Sea. Putative symbioses between Bacteria, Archaea, and ciliates observed along these oxyclines suggests a strategy of cooperative metabolism for survival that includes chemosynthetic autotrophy and exchanges of metabolic intermediates or end products between hosts and their prokaryotic partners.     

The phylogeny of endolithic microbes associated with marine basalts

We examined the phylogenetic diversity of microbial communities associated with marine basalts, using over 300 publicly available 16S rDNA sequences and new sequence data from basalt enrichment cultures. Phylogenetic analysis provided support for 11 monophyletic clades originating from ocean crust (sediment, basalt and gabbro). Seven of the ocean crust clades (OCC) are bacterial, while the remaining four OCC are in the Marine Group I (MGI) Crenarchaeota. Most of the OCC were found at diverse geographic sites, suggesting that these microorganisms have cosmopolitan distributions. One OCC in the Crenarchaeota consisted of sequences derived entirely from basalts. The remaining OCC were found in both basalts and sediments. The MGI Crenarchaeota were observed in all studies where archaeal diversity was evaluated. These results demonstrate that basalts are occupied by cosmopolitan clades of microorganisms that are also found in marine sediments but are distinct from microorganisms found in other marine habitats, and that one OCC in the ubiquitous MGI Crenarchaeota clade may be an ecotype specifically adapted to basalt.     

Cost/benefit and the effect of sample preservation procedures on quantitative patterns in benthic ecology

Some benthic assemblages studies have tested the effects of different preservation procedures on biomass, but their influence on quantitative patterns (number of species and abundance) is still unclear. We evaluated the influence of two sample preservation procedures on quantitative patterns in benthic ecology. Ten sampling points were systematically interspersed on two types of sediment (sandy and muddy). At each sediment type, samples from five sampling points were fixed in 10% formalin, and the other five points were preserved in 70% ethanol (without previous fixation). Three replicates were collected at each sampling point, and samples were washed in 0.5 mesh size and sorted in laboratory. A cost/benefit analysis was performed considering the washing time in laboratory and the costs of substances. A total of 1970 individuals were collected (muddy sediment: 132; sandy sediment: 1838), belonging to 121 taxa (muddy: 49; sandy: 83). Assemblages preserved in ethanol were composed of 795 individuals and 80 taxa, while those fixed with formalin had 1173 individuals and 94 taxa. Polychaeta predominated as the most abundant group for both preservation procedures. For the whole benthic community, significant differences occurred only between sediment types. Significant differences in the number of individuals of polychaetes were observed for the different preservation procedures in sandy sediment. Ethanol has the best cost/benefit ratio in both sediment types due to additional costs to attend safety requirements for formalin-fixed samples. Further studies should evaluate how quantitative patterns are affected by exposure time of preservation, anesthesia interaction, and morphological deformations (e.g. impossibility of identification).     

Phylogenetic analysis of southern hemisphere flat oysters based on partial mitochondrial 16S rDNA gene sequences

Oysters are among the most familiar, best studied, and morphologically variable of all marine invertebrate taxa. However, our knowledge of oyster phylogeny and systematics is rudimentary, especially for the subfamily Ostreinae (flat oysters). It is unclear, for instance, whether the predominant flat oysters occurring between latitudes 35 and 50 degrees S constitute a single circumglobal species, or multiple, phylogenetically distinct, regional taxa. We have performed the first DNA molecular phylogenetic analysis of ostreinid taxa to distinguish among competing phylogenetic and systematic hypotheses for Southern Hemisphere Ostreinae. An approximately 450-nucleotide fragment of the mitochondrial large ribosomal subunit (16S) was sequenced for 41 individual oysters, representing 14 taxa of brooding oysters: 5 Southern Hemisphere Ostreinae, 5 Northern Hemisphere Ostreinae, and 4 outgroup species of the subfamily Lophinae. Phylogenetic analyses of the resulting data set yielded consensus tree topologies that are comprehensively incongruent with prevailing morphologically based interpretations of systematic relationships among the Ostreinae. Three ostreinid mitochondrial clades were evident, each containing representatives of Southern Hemisphere regional ostreinid taxa, some of which robustly cocluster with Northern Hemisphere taxa. These three clades represent the first well-supported phylogenetic framework for this ecologically prominent and commercially important oyster subfamily.     

Advances in the study of benthic marine algae since the time of E. M. Holmes

E. M. Holmes's major interests in the marine benthic algae were, like those of most of his contemporaries, taxonomic and floristic; he was much occupied with the acquisition, for areas of the British Isles, of new records of species known already elsewhere. Records established by Holmes and his contemporaries have increasingly been subjected to examination by means of more recent laboratory and field techniques. Data thus gathered continue to reveal connections between taxa hitherto considered distinct; it is mainly this revealed capacity for structural and reproductive variation, at many levels, in the benthic marine algae that has led to amendment by posterity of earlier taxonomic opinions. Even in the areas widi a long tradition of benthic marine phycological study, there remains much to be understood; apart from the need for more workers and for yet more sophisticated research techniques, the biotic situation is itself dynamic. Nevertheless, the importance of the ground work achieved and herbaria assembled by Holmes and his contemporaries (especially Batters) cannot be denied.     

Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

Metal-sulfides are wide-spread in marine benthic habitats. At deep-sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene-based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate-reducing Nitrospirae and sulfide-oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr-clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide-oxidizers potentially facilitating metal-sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats.     

Benthic and hyporheic macroinvertebrate distribution within the heads and tails of riffles during baseflow conditions

The distribution of lotic fauna is widely acknowledged to be patchy reflecting the interaction between biotic and abiotic factors. In an in situ field study, the distribution of benthic and hyporheic invertebrates in the heads (downwelling) and tails (upwelling) of riffles were examined during stable baseflow conditions. Riffle heads were found to contain a greater proportion of interstitial fine sediment than riffle tails. Significant differences in the composition of benthic communities were associated with the amount of fine sediment. Riffle tail habitats supported a greater abundance and diversity of invertebrates sensitive to fine sediment such as EPT taxa. Shredder feeding taxa were more abundant in riffle heads suggesting greater availability of organic matter. In contrast, no significant differences in the hyporheic community were recorded between riffle heads and tails. We hypothesise that clogging of hyporheic interstices with fine sediments may have resulted in the homogenisation of the invertebrate community by limiting faunal movement into the hyporheic zone at both the riffle heads and tails. The results suggest that vertical hydrological exchange significantly influences the distribution of fine sediment and macroinvertebrate communities at the riffle scale.     

海洋沉积物中重金属对底栖无脊椎动物的生物有效性

海洋沉积物是重金属的重要贮库,而海洋底栖无脊椎动物主要从沉积物中摄取重金属,这些被摄取的重金属能够通过食物链进行传递,进而影响到人类健康。本文总结了近些年来在海洋沉积物中重金属对底栖无脊椎动物生物有效性方面的研究进展,包括海洋底栖无脊椎动物对重金属的吸收途径、沉积物地球化学性质和底栖无脊椎动物生理等生物因素对沉积物中重金属生物有效性的影响。在此基础上,展望了未来研究重点,主要包括近海富营养化对沉积物中重金属生物有效性的影响,海洋底栖无脊椎动物消化道中的物理消化过程对沉积物中重金属生物有效性的影响,海洋底栖无脊椎动物整个生活史过程中沉积物中重金属生物有效性的变化等。     

Patterns in marine hydrozoan richness and biogeography around southern Africa: implications of life cycle strategy

Aim To examine patterns of marine hydrozoan richness around southern Africa and to test the hypothesis that patterns of biogeography become weaker with increasing dispersal ability. Location The coastline of southern Africa from 21° S, 14° E to 28° S, 33° E, extending from the intertidal zone seawards a distance of 200 nautical miles. Methods Published and unpublished information on the distribution of marine Hydrozoa was entered as presence/absence data onto a gridded coastline of the region. A similarity matrix between the species composition of grid squares was constructed using the Bray–Curtis index and visualized using non-metric multidimensional scaling ordinations. Separate analyses were conducted, and compared, on the three major life cycle groupings: holoplanktic, meroplanktic and benthic. Results Over 450 species of marine Hydrozoa have been reported from the region, and species richness increases eastwards, in a manner at odds with the distribution of sampling effort. There was a significant correlation between the geographic structures of the resemblance matrices generated for the three life cycle groupings. In other words, all three groups showed similar patterns of biogeography around the region, and these were broadly similar to those reported by others. However, there were differences between them that reflect the resolution at which the data were examined. At a level of 40% similarity, there was no biogeographic structure to the holoplanktic fauna, the meroplanktic taxa were simply sub-divided into cool- and warm-temperate/subtropical elements, and in the case of benthic taxa, the cool-water fauna was further split into a southern Namaqua and a depauperate northern Namib component. Even at a resolution of 70% similarity, the holopelagic taxa could be separated only into cool-temperate and warm-temperate/subtropical faunas. Main conclusions Holoplanktic taxa show comparatively less biogeographic structure than meroplanktic taxa, which in turn show less clearly defined biogeographic structure than benthic taxa. It is suggested that this is related to the interaction between oceanography and dispersive-stage duration. The role that the Agulhas Current plays in influencing the Benguela Current fauna is highlighted. This study has implications for conservation planning exercises based on protecting representative biotopes in different biogeographic regions.     

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and β-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzyme-producing organisms had a maximum phylogenetic depth of 0.008004–0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04–98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.     

The latitudinal position of peak marine diversity in living and fossil biotas

Aim Peak marine taxonomic diversity has only rarely occurred at or near the equator during the Phanerozoic Eon, in contrast to the present‐day pattern. This fundamental difference is difficult to reconcile because the latitude at which peak diversity occurs for living marine taxa has not yet been explicitly determined at a broad taxonomic and spatial scale. Here, we attempt to determine this value in order to compare the contemporary and fossil patterns directly. Location Our data are global in coverage. Methods We used a literature compilation of 149 present‐day marine latitudinal diversity gradients. We summed the number of marine taxa that exhibited peak diversity within 10° latitudinal bins. In addition, we recorded locality data, general habitat (benthic/pelagic), and the taxonomic level of the study organisms. Results We found that peak diversity for most sampled marine taxa currently occurs between 10° and 20° N, even after correcting for a Northern Hemisphere sampling bias. Moreover, this peak position is a global phenomenon: it is found across habitats and higher taxa, within all sampled ocean basins, and on both sides of the Atlantic and Pacific oceans. Benthic taxa, which dominate our data, exhibit one peak at 10°–20° N, while pelagic taxa exhibit a peak at 10°–20° N and an additional peak at 10°–20° S, producing a distinct trough at the equator. Main conclusions Our data indicate that peak marine diversity for many taxa is currently within 10°–20° N rather than at the equator, and that this is not likely to result from either undersampling at lower latitudes or the pattern being dominated by a particular taxon. Possible explanations may include a coincidence with the intertropical convergence zone, a mid‐domain effect, abundant shallow marine habitat, or high ocean temperatures at latitudes nearest the equator. Regardless of its exact cause, the position of peak diversity should be considered a fundamental feature of the latitudinal diversity gradient that must be accounted for within attempts to explain the latter’s existence.     

Reliability of CARD-FISH Procedure for Enumeration of Archaea in Deep-Sea Surficial Sediments

The enumeration of Archaea in deep-sea sediment samples is still limited, although different methodological procedures have been applied. Among these, catalysed reporter deposition-fluorescence in situ hybridisation (CARD-FISH) technique is a promising tool for estimation of archaeal abundance in deep-sea sediment samples. Comparing different permeabilisation treatments, the best results obtained both on archaeal pure cultures and on natural assemblages were with hydrochloric acid (0.1 M) and proteinase K (0.004 U/ml) treatments. The application of CARD-FISH on deep-sea sediments revealed that Archaea reach up to 41% of total prokaryotic cells. Specific probes for planktonic Archaea showed that marine Crenarchaea dominated archaeal seafloor communities. No clear bathymetric trends were observed for archaeal abundances and the morphology of continental margin (slope vs. canyon) seems not to have a direct influence on archaeal relative abundances. The site-specific sediment habitat—both abiotic environmental setting and sedimentary organic matter quality—explain up to 65% of variance of archaeal, crenarchaeal and euryarchaeal relative abundance, suggesting a wide ecophysiological adaptation to deep-sea benthic ecosystems. The findings demonstrate that Archaea are an important component of benthic microbial assemblages so far neglected, and hence they lay the groundwork for more focused research on their ecological importance in the functioning of deep-sea benthic ecosystems.     

Spatial distribution of live benthic foraminifera in the Rhône prodelta: Faunal response to a continental–marine organic matter gradient

Benthic foraminifera were collected in the Rhône prodelta (Gulf of Lions, Mediterranean Sea), an enriched zone with high organic matter content. In June 2005, sediment cores were sampled at depths ranging from 20 to 100 m. Four distinct foraminiferal assemblages were determined in the study area, reflecting the geographical distribution of the impact of river supply. The living foraminiferal faunas present a typical picture, with strongly impoverished faunas composed exclusively of stress-tolerant taxa (Fursenkoina fusiformis, Bulimina aculeata, Leptohyalis scottii, and Adelosina longirostra) in the immediate vicinity of the river mouth. This assemblage is well adapted to a high input of continental organic matter and a minimum oxygen penetration depth into the sediment. To the southwest, under the main corridor followed by the river plume, high organic input with a dominantly terrestrial signature (more refractory) may be stressful for many taxa which need organic matter of a more labile quality. In this area, Nonion scaphum, Nonionella turgida and Rectuvigerina phlegeri are present in low densities. On the edge of this area, these taxa show much higher densities. A greater proportion of marine organic carbon could explain their increasing abundances in this area. Towards the east and towards the deepest stations, in the outer part of the enriched zone, biodiversity increases. Faunas at these stations have intermediate densities and contain a number of taxa (Cassidulina carinata, Epistominella vitrea, Valvulineria bradyana, Nonionella iridea/bradyi) at the deepest stations; Bolivina dilatata/spathulata and Textularia porrecta at the eastern stations) that seem to benefit from more marine organic matter. The comparison of geochemical measurements and foraminiferal data strongly suggests that the spatial distribution of foraminifera in the Rhône prodelta is mainly governed by the quality and the quantity of organic matter reaching the sediment–water interface. Since bottom waters are well oxygenated (215–260 µmol/L), and oxygen penetration into the sediment is less than 1 cm at all stations, benthic ecosystem oxygenation appears to have only a minor impact on regional differences in faunal distribution.     

Convergent photophysiology and prokaryotic assemblage structure in epilithic cyanobacterial tufts and algal turf communities

As global change spurs shifts in benthic community composition on coral reefs globally, a better understanding of the defining taxonomic and functional features that differentiate proliferating benthic taxa is needed to predict functional trajectories of reef degradation better. This is especially critical for algal groups, which feature dramatically on changing reefs. Limited attention has been given to characterizing the features that differentiate tufting epilithic cyanobacterial communities from ubiquitous turf algal assemblages. Here, we integrated an in situ assessment of photosynthetic yield with metabarcoding and shotgun metagenomic sequencing to explore photophysiology and prokaryotic assemblage structure within epilithic tufting benthic cyanobacterial communities and epilithic algal turf communities. Significant differences were not detected in the average quantum yield. However, variability in yield was significantly higher in cyanobacterial tufts. Neither prokaryotic assemblage diversity nor structure significantly differed between these functional groups. The sampled cyanobacterial tufts, predominantly built by Okeania sp., were co-dominated by members of the Proteobacteria, Firmicutes, and Bacteroidota, as were turf algal communities. Few detected ASVs were significantly differentially abundant between functional groups and consisted exclusively of taxa belonging to the phyla Proteobacteria and Firmicutes. Assessment of the distribution of recovered cyanobacterial amplicons demonstrated that alongside sample-specific cyanobacterial diversification, the dominant cyanobacterial members were conserved across tufting cyanobacterial and turf algal communities. Overall, these data suggest a convergence in taxonomic identity and mean photosynthetic potential between tufting epilithic cyanobacterial communities and algal turf communities, with numerous implications for consumer-resource dynamics on future reefs and trajectories of reef functional ecology.     

Morphological and developmental macroevolution: a paleontological perspective

Evidence of the morphological evolution of metazoans has been preserved, in varying degrees of completeness, in the fossil record of the last 600 million years. Although extinction has been incessant at lower taxonomic levels, genomic comparisons among surviving members of higher taxa suggest that much of the developmental systems that pattern their bodyplans has been conserved from early in their history. Comparisons between the origin of morphological disparity in the record and patterns of genomic disparity among living taxa promise to be interesting. For example, Hox cluster composition varies among major taxa, and the fossil record suggests that many of the changes in Hox clusters may have been associated with late Neoproterozoic evolution among minute benthic vermiform clades, from which crown bilaterian phyla arose just before or during the Cambrian explosion. Study of genomic differences among crown classes and orders whosetiming and mode of origin can be inferred from morphological data inthefossil record should throw further light on the timing and mode of origin of genomic disparities.     

Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences

The extracellular DNA pool in marine sediments is the largest reservoir of DNA of the world oceans and it potentially represents an archive of genetic information and gene sequences involved in natural transformation processes. However, no information is at present available for the gene sequences contained in the extracellular DNA and for the factors that influence their preservation. In the present study, we investigated the depurination and degradation rates of extracellular DNA in a variety of marine sediment samples characterized by different ages (up to 10 000 years) and environmental conditions according to the presence, abundance and diversity of prokaryotic gene sequences. We provide evidence that depurination of extracellular DNA in these sediments depends upon the different environmental factors that act synergistically and proceeds at much slower rates than those theoretically predicted or estimated for terrestrial ecosystems. These findings suggest that depurination in marine sediments is not the main process that limits extracellular DNA survival. Conversely, DNase activities were high suggesting a more relevant role of biologically driven processes. Amplifiable prokaryotic 16S rDNA sequences were present in most benthic systems analysed, independent of depurination and degradation rates and of the ages of the sediment samples. Additional molecular analyses revealed that the extracellular DNA pool is characterized by relatively low-copy numbers of prokaryotic 16S rDNA sequences that are highly diversified. Overall, our results suggest that the extracellular DNA pool in marine sediments represents a repository of genetic information, which can be used for improving our understanding of the biodiversity, functioning and evolution of ecosystems over different timescales.