The Vertical Distribution and Diversity of Marine Bacteriophage at a Station off Southern California

Sixty-two bacteriophages were isolated on eight indigenous bacteria from a Pacific Ocean station spanning 887-m vertical depth, on two occasions between 1999 and 2000. On the basis of 16S rRNA sequences, six hosts were tentatively identified to be in the genus Vibrio and the other two were closely related to Altermonas macleodii (W9a) and Pseudoalteromonas spp. (W13a). Restriction fragment length polymorphism (RFLP) analysis of phage genomes using AccI and HapI showed that 16 phages infecting host C4a (Vibrio) displayed 14 unique RFLP patterns. However, identical phages infecting host C4b, C6a, and C6b (all Vibrio) were obtained from both the surface layer and the hypoxic zone at 850 m. Most phage isolates from the second year had a different RFLP pattern but shared genetic similarity to the phages infecting the same host from the previous year based on a hybridization study using phage genome probes. Cluster analysis of RFLP patterns and hybridization results also indicated that phages infecting the same or genetically related hosts, in general, shared higher degrees of homology in spite of the diverse RFLP patterns. Pulsed field gel electrophoresis (PFGE) analysis of native viral genomes indicated a range in genome size from less than 40 to 200 kb, and the dominant band shifted up by about 5-10 kb in the deep samples compared to the shallow ones. Hybridization of phage genome probes with total viral community DNA from various depths suggests these isolates, or at least some of their genes, represent a detectable portion of the natural viral community and were distributed throughout the water column. Thus, the results of this study demonstrated that the genetic diversity of bacteriophage in the ocean is far greater than that of their bacterial hosts. However, host range may have contributed to the evolution of the diverse phage population in the marine environment.     

A Short-Term Study of Vertical and Horizontal Distribution of Zooplankton During Thermal Stratification in Lake Kinneret,Israel

This study documents for the first time both vertical and horizontal distribution patterns of the zooplankton community in Lake Kinneret during the period of thermal stratification. The zooplankton distribution patterns were explored in relation to abiotic (temperature, oxygen) and biotic (picocyanobacteria, ciliates, flagellates, phytoplankton, fish) environmental gradients. Sampling was carried out on 6–7 July 1992 at five stations and six depths from nearshore to offshore. Zooplankton abundance and biomass varied from 5 to 267 ind. l^–1(mean: 95 ind. l^–1), and from 0.1 to 65 d.w. mg m^–3(mean: 24 d.w. mg m^–3). Zooplankton taxonomic groups (Rotifera, Cladocera, Cyclopoida, Calanoida) and size classes (micro-, meso- and macrozooplankton) showed peaks of maximal density and biomass in the epilimnetic and metalimnetic strata (5 and 14 m). Depth, accounting for 31–39% of total spatial variation, reflected the vertical distribution of zooplankton in relation to temperature and oxygen declines, and the higher concentration of food resources (protists and phytoplankton) in the epilimnion and metalimnion. Onshore–offshore distance, accounting for 17–22% of the total spatial variance, reflected different distribution patterns shown among zooplankton groups and size classes. The macrozooplankton (Copepoda, Cladocera) was more abundant offshore, whereas microzooplankton (Rotifera and nauplii) predominated nearshore. These horizontal distribution patterns were related to small increases in temperature and phytoplankton biomass, and higher concentrations of fish in the littoral zone. Although limited to a short temporal scale, our study indicated that zooplankton spatial distribution in Lake Kinneret during the period of thermal stratification was related to physicochemical, food and predation factors, manifested differently along the vertical and nearshore–offshore gradients.     

Localisation of Nursery Areas Based on Comparative Analyses of the Horizontal and Vertical Distribution Patterns of Juvenile Baltic Cod (Gadus morhua)

Knowledge of the spatial distribution of juvenile cod is essential for obtaining precise recruitment data to conduct sustainable management of the eastern and western Baltic cod stocks. In this study, the horizontal and vertical distribution and density patterns of settled juvenile 0- and 1-group Baltic cod are determined, and their nursery areas are localised according to the environmental factors affecting them. Comparative statistical analyses of biological, hydrographic and hydroacoustic data are carried out based on standard ICES demersal trawl surveys and special integrated trawl and acoustic research surveys. Horizontal distribution maps for the 2001–2010 cohorts of juvenile cod are further generated by applying a statistical log-Gaussian Cox process model to the standard trawl survey data. The analyses indicate size-dependent horizontal and distinct vertical and diurnal distribution patterns related to the seabed topography, water layer depth, and the presence of hydrographic frontal zones (pycnoclines) as well as intraspecific patterns in relation to the presence of adult cod. The extent of the nursery areas also depends on the cod year class strength. Juvenile cod (≥3 cm) are present in all areas of the central Baltic Sea (CBS), showing broad dispersal. However, their highest density in the Baltic Basins is found at localities with a 40–70 m bottom depth in waters with oxygen concentrations above 2 ml O₂.l⁻¹ and temperatures above 5°C. The smallest juveniles are also found in deep sea localities down to a 100 m depth and at oxygen concentrations between 2–4 ml O₂.l⁻¹. The vertical, diurnally stratified and repeated trawling and hydroacoustic target strength-depth distributions obtained from the special surveys show juvenile cod concentrations in frontal zone water layers (pycnocline). However, the analyses indicate that in the CBS, juvenile cod of all sizes do not appear to aggregate in dense schooling patterns, which differs from what has been reported from the North Sea.     

Vertical and Horizontal Distribution of Bacterial Communities in Alluvial Groundwater of the Nakdong River Bank

As a collaborative effort to characterize a pilot test site for managed aquifer recharge (MAR), vertical and horizontal distributions of microbial communities in the river bank subsurface were investigated to assess the ecological effects after the operation of the MAR using the river water adjacent to the site. Along with a geochemical analysis, barcoded pyrosequencing was performed using the genomic DNAs extracted from the subsurface groundwater/sediment samples retrieved from three multilevel wells among the installed cluster of 14 boreholes. A total of 9 samples from 3 depths (10, 15–25, and 33 m below the ground surface) of each borehole showed higher bacterial abundance and diversity in the shallow (10 m) depths than in the deep (33 m) groundwater. In addition, there was a slight separation of the microbial communities between the depths based on the nonmetric multidimensional scaling analysis of the Yue and Clayton distance and the distance-weighted UniFrac analysis. The phylum Proteobacteria was dominant in all the samples at the sequence abundance of 64.0–97.8% with the total operational taxonomic units of 3375 at the species level, while among the total 288 genera, the genus Pseudomonas and an unclassified genus from Betaproteobacteria were the most abundant across the samples. The community separation between the shallow and the deep groundwater seemed to be correlated with depth differences, supported by differences in the dissolved oxygen (DO) concentration and oxidation-reduction potential (ORP). In the study site, unusually high values of electrical conductivity (EC) were found in the deep groundwater, but those values were unlikely to contribute to the community separation between the shallow and deep groundwater, unlike the DO and ORP values, which were found to influence the community differences.     

Vertical Migration and Mortality of Marine Benthos in Dredged Material: A Synthesis

This account describes the comparative response of four species of benthic invertebrates to burial in terms of vertical migration and mortality, and provides a synthesis of studies and recommendations upon which to assess future impacts. The species featured were the bivalve Mercenaries mercenaria, the amphipod crustacean Parahaustorius longimerus, and the polychaetes Scoloplos fragilis and Nereis succinea. There was evidence of synergistic effects on burrowing activity and mortality with changes in time of burial, sediment depth, sediment type and temperature. In sediment with silt-clay, N. succinea was the most resistant species followed by M. mercenaria, S. fragilis and P. longimerus. In sediment without silt-clay the order of percent mortality was reversed. Studies of surface water chemistry and sediment geochemistry showed that dissolved oxygen decreased significantly and ammonia and sulfide increased significantly between the surface and below 2.0 cm within a 15-day period. Based on these results and physiological tolerances from the literature it was concluded that M. mercenaria and N. succinea would be relatively resistant to chemical effects of spoil disposal, whereas S. fragilis and P. longimerus would be less resistant to such effects. Vertical migration of benthic invertebrates through dredge disposal can be a viable mechanism of recolonization under certain conditions. Some effects of burial of benthos can be predicted based on morphology, behavior and physiology. These biological features were discussed with examples dealing with molluscs, crustaceans, and polychaetes. Finally, recommendations were made concerning the type of studies to provide additional data to aid management agencies in decision making about future dredging and disposal practices.     

Squidpops: A Simple Tool to Crowdsource a Global Map of Marine Predation Intensity

We present a simple, standardized assay, the squidpop, for measuring the relative feeding intensity of generalist predators in aquatic systems. The assay consists of a 1.3-cm diameter disk of dried squid mantle tethered to a rod, which is either inserted in the sediment in soft-bottom habitats or secured to existing structure. Each replicate squidpop is scored as present or absent after 1 and 24 hours, and the data for analysis are proportions of replicate units consumed at each time. Tests in several habitats of the temperate southeastern USA (Virginia and North Carolina) and tropical Central America (Belize) confirmed the assay’s utility for measuring variation in predation intensity among habitats, among seasons, and along environmental gradients. In Belize, predation intensity varied strongly among habitats, with reef > seagrass = mangrove > unvegetated bare sand. Quantitative visual surveys confirmed that assayed feeding intensity increased with abundance and species richness of fishes across sites, with fish abundance and richness explaining up to 45% and 70% of the variation in bait loss respectively. In the southeastern USA, predation intensity varied seasonally, being highest during summer and declining in late autumn. Deployments in marsh habitats generally revealed a decline in mean predation intensity from fully marine to tidal freshwater sites. The simplicity, economy, and standardization of the squidpop assay should facilitate engagement of scientists and citizens alike, with the goal of constructing high-resolution maps of how top-down control varies through space and time in aquatic ecosystems, and addressing a broad array of long-standing hypotheses in macro- and community ecology.     

四川省峨眉山森林植被垂直分布的初步研究

本文对四川省峨眉山森林植被的垂直分布特点进行了初步研究。文中,采用数量分类的方法,结合对群落生态外貌特点和区系组成的分析,以及群落所处海拔高度,划分出森林植被的垂直带如下：1．常绿阔叶林带 1900米以下;2．常绿、落叶阔叶混交林带 1500米至2000米;3．针阔混交林带 2000米至2500米;4．寒温性针叶林带 2500米至3099米。     

Global Patterns in Ecological Indicators of Marine Food Webs: A Modelling Approach

Background

Ecological attributes estimated from food web models have the potential to be indicators of good environmental status given their capabilities to describe redundancy, food web changes, and sensitivity to fishing. They can be used as a baseline to show how they might be modified in the future with human impacts such as climate change, acidification, eutrophication, or overfishing.

Methodology

In this study ecological network analysis indicators of 105 marine food web models were tested for variation with traits such as ecosystem type, latitude, ocean basin, depth, size, time period, and exploitation state, whilst also considering structural properties of the models such as number of linkages, number of living functional groups or total number of functional groups as covariate factors.

Principal findings

Eight indicators were robust to model construction: relative ascendency; relative overhead; redundancy; total systems throughput (TST); primary production/TST; consumption/TST; export/TST; and total biomass of the community. Large-scale differences were seen in the ecosystems of the Atlantic and Pacific Oceans, with the Western Atlantic being more complex with an increased ability to mitigate impacts, while the Eastern Atlantic showed lower internal complexity. In addition, the Eastern Pacific was less organised than the Eastern Atlantic although both of these systems had increased primary production as eastern boundary current systems. Differences by ecosystem type highlighted coral reefs as having the largest energy flow and total biomass per unit of surface, while lagoons, estuaries, and bays had lower transfer efficiencies and higher recycling. These differences prevailed over time, although some traits changed with fishing intensity. Keystone groups were mainly higher trophic level species with mostly top-down effects, while structural/dominant groups were mainly lower trophic level groups (benthic primary producers such as seagrass and macroalgae, and invertebrates). Keystone groups were prevalent in estuarine or small/shallow systems, and in systems with reduced fishing pressure. Changes to the abundance of key functional groups might have significant implications for the functioning of ecosystems and should be avoided through management.

Conclusion/significance

Our results provide additional understanding of patterns of structural and functional indicators in different ecosystems. Ecosystem traits such as type, size, depth, and location need to be accounted for when setting reference levels as these affect absolute values of ecological indicators. Therefore, establishing absolute reference values for ecosystem indicators may not be suitable to the ecosystem-based, precautionary approach. Reference levels for ecosystem indicators should be developed for individual ecosystems or ecosystems with the same typologies (similar location, ecosystem type, etc.) and not benchmarked against all other ecosystems.     

Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale

Aflatoxins are produced by Aspergillus flavus and A. parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture, with aflatoxin B₁ being the most carcinogenic natural compound known. Sexual reproduction in these species occurs between individuals belonging to different vegetative compatibility groups (VCGs). We examined natural genetic variation in 758 isolates of A. flavus, A. parasiticus and A. minisclerotigenes sampled from single peanut fields in the United States (Georgia), Africa (Benin), Argentina (Córdoba), Australia (Queensland) and India (Karnataka). Analysis of DNA sequence variation across multiple intergenic regions in the aflatoxin gene clusters of A. flavus, A. parasiticus and A. minisclerotigenes revealed significant linkage disequilibrium (LD) organized into distinct blocks that are conserved across different localities, suggesting that genetic recombination is nonrandom and a global occurrence. To assess the contributions of asexual and sexual reproduction to fixation and maintenance of toxin chemotype diversity in populations from each locality/species, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 mating-type individuals, which is indicative of a sexually recombining population. All samples were clone-corrected using multi-locus sequence typing which associates closely with VCG. For both A. flavus and A. parasiticus, when the proportions of MAT1-1 and MAT1-2 were significantly different, there was more extensive LD in the aflatoxin cluster and populations were fixed for specific toxin chemotype classes, either the non-aflatoxigenic class in A. flavus or the B₁-dominant and G₁-dominant classes in A. parasiticus. A mating type ratio close to 1∶1 in A. flavus, A. parasiticus and A. minisclerotigenes was associated with higher recombination rates in the aflatoxin cluster and less pronounced chemotype differences in populations. This work shows that the reproductive nature of the population (more sexual versus more asexual) is predictive of aflatoxin chemotype diversity in these agriculturally important fungi.     

基于地面调查与遥感调查协同的城市绿地规模和分布研究——以青岛市为例

城市绿地调查作为园林绿化规划建设管理的基础工作,其数据准确程度直接影响着城市园林绿化的科学发展。提出了基于遥感调查与地面调查协同的城市绿地调查的技术方法,通过该方法获得数据与单独使用遥感调查或地面调查技术获得数据相比提升了城市绿地,尤其是公园绿地和附属绿地调查的时效性和准确性,为城市绿地调查提供了可操作的技术方法。     

Spatial Distribution of Rhodopseudomonas palustris Ecotypes on a Local Scale

The number, spatial distribution, and significance of genetically distinguishable ecotypes of prokaryotes in the environment are poorly understood. Oda et al. (Y. Oda, B. Star, L. A. Huisman, J. C. Gottschal, and L. J. Forney, Appl. Environ. Microbiol. 69:xxx-xxx, 2003) have shown that Rhodopseudomonas palustris ecotypes were lognormally distributed along a 10-m transect and that multiple strains of the species could coexist in 0.5-g sediment samples. To extend these observations, we investigated the clonal diversity of R. palustris in 0.5-g samples taken from the corners and center of a 1-m square. A total of 35 or 36 clones were recovered by direct plating from each sample and were characterized by BOX A1R repetitive element-PCR genomic DNA fingerprinting. Isolates with fingerprint images that were ≥80% similar to each other were defined as the same genotype. Among the 178 isolates studied, 32 genotypes were identified, and each genotype contained between 1 and 40 isolates. These clusters were consistent with minor variations found in 16S rRNA gene sequences. The Shannon indices of the genotypic diversity within each location ranged from 1.08 (5 genotypes) to 2.18 (13 genotypes). Comparison of the rank abundance of genotypes found in pairs of locations showed that strains from three locations were similar to each other, with Morisita-Horn similarity coefficients ranging from 0.59 to 0.71. All comparisons involving the remaining two locations resulted in coefficients between 0 and 0.12. From these results we inferred that the patterns of ecotype diversity at the sampling site are patchy at a 1-m scale and postulated that factors such as mixing, competitive interactions, and microhabitat variability are likely to be responsible for the maintenance of the similarities between some locations and the differences between others.     

Vertical Distribution of Bacteria and Algae in a Tropical Lake

In another paper (SCHMIDT, 1969b) the relations between the numbers of bacteria and phytoplankton in the surface layers of some waters near Manaus (Amazonas) were reported. As a stratification of phytoplankton is not possible, due to the strong turbulence in the Rio Solimões (Amazon River), and since current was also present in the Rio Negro off the bays and littoral regions, the vertical distribution of bacteria and algae was of special interest in the Lago do Castanho, the third of the waterbodies investigated in the paper mentioned above. In the present study, two important fractions of bacteria, their total number, and the fraction of saprophyta (estimated by the number of bacterial colonies), were also differentiated.     

Local Scale Comparisons of Biodiversity as a Test for Global Protected Area Ecological Performance: A Meta-Analysis

Terrestrial protected areas (PAs) are cornerstones of global biodiversity conservation. Their efficacy in terms of maintaining biodiversity is, however, much debated. Studies to date have been unable to provide a general answer as to PA conservation efficacy because of their typically restricted geographic and/or taxonomic focus, or qualitative approaches focusing on proxies for biodiversity, such as deforestation. Given the rarity of historical data to enable comparisons of biodiversity before/after PA establishment, many smaller scale studies over the past 30 years have directly compared biodiversity inside PAs to that of surrounding areas, which provides one measure of PA ecological performance. Here we use a meta-analysis of such studies (N = 86) to test if PAs contain higher biodiversity values than surrounding areas, and so assess their contribution to determining PA efficacy. We find that PAs generally have higher abundances of individual species, higher assemblage abundances, and higher species richness values compared with alternative land uses. Local scale studies in combination thus show that PAs retain more biodiversity than alternative land use areas. Nonetheless, much variation is present in the effect sizes, which underscores the context-specificity of PA efficacy.     

Global Distribution of Campylobacter jejuni Penner Serotypes: A Systematic Review

Penner serotyping has been the principal method for differentiating Campylobacter isolates since its inception. Campylobacter capsule polysaccharide (CPS), the principal serodeterminant on which Penner serotyping is based, is presently of interest as a vaccine component. To determine the required valency of an effective CPS-based vaccine, a comprehensive understanding of CPS distribution is needed. Because of the association between Penner serotype and CPS, we conducted a systematic review to estimate the frequency and distribution of Penner serotypes associated with cases of Campylobacteriosis. In total, more than 21,000 sporadic cases of C. jejuni cases were identified for inclusion. While regional variation exists, distribution estimates indicate that eight serotypes accounted for more than half of all sporadic diarrheal cases globally and three serotypes (HS4 complex, HS2, and HS1/44) were dominant inter-regionally as well as globally. Furthermore, a total of 17 different serotypes reached a representation of 2% or greater in at least one of the five regions sampled. While this review is an important first step in defining CPS distribution, these results make it clear that significant gaps remain in our knowledge. Eliminating these gaps will be critical to future vaccine development efforts.     

Global Distribution and Evolution of a Toxinogenic Burkholderia-Rhizopus Symbiosis

Toxinogenic endobacteria were isolated from a collection of Rhizopus spp. representing highly diverse geographic origins and ecological niches. All endosymbionts belonged to the Burkholderia rhizoxinica complex according to matrix-assisted laser desorption ionization-time of flight biotyping and multilocus sequence typing, suggesting a common ancestor. Comparison of host and symbiont phylogenies provides insights into possible cospeciation and horizontal-transmission events.Bacterial symbionts and their metabolic potential play essential roles for many organisms. They may benefit from improved fitness, survival, and even acquired virulence (7, 12, 22). In the course of our studies of the biosynthesis of rhizoxin, the causative agent of rice seedling blight (10), we found that the phytotoxin is produced not by the fungus Rhizopus microsporus but by symbiotic bacteria (Burkholderia rhizoxinica) that reside within the fungus cytosol (13, 15, 23). Furthermore, cloning and sequencing of the rhizoxin biosynthesis gene cluster revealed the molecular basis of bacterial toxin production (14). In sum, this represents an unparalleled example for a symbiosis in which a fungus harbors bacteria for the production of a virulence factor. In analogy, we found that the first reported “mycotoxins” from lower fungi, the highly toxic cyclopeptides rhizonin A and B (25, 28), are also produced by symbiotic bacteria (Burkholderia endofungorum) and not by the fungus (16). While both rhizoxins and rhizonins have been believed to promote zygomycoses (21), there is no indication for toxin-producing endosymbiotic bacteria in clinical isolates (18).In nature, toxin production plays a pivotal role in the development of the fungus-bacterium association. Studies of the evolution of host resistance indicate that the association resulted from a pathogenicity mutualism shift in insensitive zygomycetes (24). The fungus lost its ability to sporulate independently and became totally dependent on endobacteria for reproduction through spores, thus warranting the persistence of the symbiosis and its efficient distribution through vegetative spores (17).To gain a broader view of the occurrence, biosynthetic potential, and relationship of toxinogenic endofungal bacteria, we investigated a collection of Rhizopus spp. consisting of 20 isolates classified as R. microsporus (of which 13 belong to R. microsporus var. microsporus, four to R. microsporus var. chinensis, two to R. microsporus var. oligosporus, and one to R. microsporus var. rhizopodiformis), one isolate classified as Rhizopus sp., and one Rhizopus oryzae strain. We initially monitored the presence of bacterial symbionts by PCR using universal primers (16S rRNA genes) and rhizoxin production in all available Rhizopus strains. Liquid cultivation of fungi in production medium with and without antibiotic followed by organic solvent extraction yielded crude extracts that were analyzed by high-performance liquid chromatography (HPLC) and mass spectrometry (MS). In total, eight fungal strains were identified or confirmed as rhizoxin positive and thus expected to harbor endosymbionts. In all cases, this assumption was verified by PCR and confocal scanning microscopy. By means of an optimized protocol, we finally succeeded in the isolation and cultivation of all eight bacterial symbiont strains in pure cultures (isolates B1 to B8) (Table ​(Table11).

TABLE 1.

Fungal strains and their bacterial endosymbionts

The Future of the Oceans Past: Towards a Global Marine Historical Research Initiative

Historical research is playing an increasingly important role in marine sciences. Historical data are also used in policy making and marine resource management, and have helped to address the issue of shifting baselines for numerous species and ecosystems. Although many important research questions still remain unanswered, tremendous developments in conceptual and methodological approaches are expected to contribute to a comprehensive understanding of the global history of human interactions with life in the seas. Based on our experiences and knowledge from the “History of Marine Animal Populations” project, this paper identifies the emerging research topics for future historical marine research. It elaborates on concepts and tools which are expected to play a major role in answering these questions, and identifies geographical regions which deserve future attention from marine environmental historians and historical ecologists.     

Biodiversity's Big Wet Secret: The Global Distribution of Marine Biological Records Reveals Chronic Under-Exploration of the Deep Pelagic Ocean

Background

Understanding the distribution of marine biodiversity is a crucial first step towards the effective and sustainable management of marine ecosystems. Recent efforts to collate location records from marine surveys enable us to assemble a global picture of recorded marine biodiversity. They also effectively highlight gaps in our knowledge of particular marine regions. In particular, the deep pelagic ocean – the largest biome on Earth – is chronically under-represented in global databases of marine biodiversity.

Methodology/Principal Findings

We use data from the Ocean Biogeographic Information System to plot the position in the water column of ca 7 million records of marine species occurrences. Records from relatively shallow waters dominate this global picture of recorded marine biodiversity. In addition, standardising the number of records from regions of the ocean differing in depth reveals that regardless of ocean depth, most records come either from surface waters or the sea bed. Midwater biodiversity is drastically under-represented.

Conclusions/Significance

The deep pelagic ocean is the largest habitat by volume on Earth, yet it remains biodiversity''s big wet secret, as it is hugely under-represented in global databases of marine biological records. Given both its value in the provision of a range of ecosystem services, and its vulnerability to threats including overfishing and climate change, there is a pressing need to increase our knowledge of Earth''s largest ecosystem.