Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring

Metagenomics refers to the analysis of DNA from a whole community. Metagenomic sequencing of environmental DNA has greatly improved our knowledge of the identity and function of microorganisms in aquatic, terrestrial, and human biomes. Although open oceans have been the primary focus of studies on aquatic microbes, coastal and brackish ecosystems are now being surveyed. Here, we review so far published studies on microbes in the Baltic Sea, one of the world’s largest brackish water bodies, using high throughput sequencing of environmental DNA and RNA. Collectively the data illustrate that Baltic Sea microbes are unique and highly diverse, and well adapted to this brackish-water ecosystem, findings that represent a novel base-line knowledge necessary for monitoring purposes and a sustainable management. More specifically, the data relate to environmental drivers for microbial community composition and function, assessments of the microbial biodiversity, adaptations and role of microbes in the nitrogen cycle, and microbial genome assembly from metagenomic sequences. With these discoveries as background, prospects of using metagenomics for Baltic Sea environmental monitoring are discussed.     

Ecological Biodiversity of Marine Nematodes in Samples from Temperate, Tropical, and Deep-Sea Regions

Little is known about the biodiversity of free-living nematodes. We have attempted to provide baseline information about the natural diversities (those not influenced by pollution) that might be expected in six biotopes. Seventeen marine nematode data sets consisting of 197 samples were standardized to allow a comparison of alpha diversity, or sample diversity, from temperate estuarine, tropical sublittoral, temperate sublittoral, bathyal, abyssal, and hadal biotopes, which were selected on criteria of depth and latitude. The diversity analysis methods we employed were rarefaction curves; three weighted diversity indices of species richness, SR, H', and ES(X); and two equitability indices, J' and V. Diversity was significantly different in the six biotopes. The weighted indices of species richness were more capable of resolving differences between the biotopes than were the equitability indices, whose large standard errors suggested that they were more influenced by local, small-scale ecological factors. This suggests that species richness is a better measure than equitability for large-scale comparisons of biotopes or regions. The ES(X), which is robust to sample size variations, was more efficient than the weighted indices of species richness, which were easily influenced by sample size. There was a nonlinear relationship between depth and diversity with the bathyal and abyssal biotopes displaying the highest diversity. The tropical sublittoral biotope was not more diverse than the temperate sublittoral biotope. The lowest diversities were found in the physically challenging temperate estuarine and hadal biotopes.     

Potential Effects of a Forest Management Plan on Bachman's Sparrows (Aimophila aestivalis): Linking a Spatially Explicit Model with GIS

By combining a spatially explicit, individual-based population simulation model with a geographic information system, we have simulated the potential effects of a U.S. Forest Service management plan on the population dynamics of Bachman's Sparrow ( Aimophila aestivalis ) at the Savannah River Site, a U.S. Department of Energy facility in South Carolina. Although the Forest Service's management plan explicitly sets management goals for many species, most of the prescribed management strategy deals with the endangered Red-cockaded Woodpecker ( Picoides borealis ) because of legal requirements. We explored how a species (the sparrow) that is not the target of specific management strategies but that shares some habitat requirements with the woodpecker, would fare under the management plan. We found that the major components of the proposed management plan may allow the sparrow population to reach and exceed the minimum management goal set for this species, but only after a substantial initial decline in sparrow numbers and a prolonged transition period. In the model, the sparrow population dynamics were most sensitive to demographic variables such as adult and juvenile survivorship and to landscape variables such as the suitability of young clearcuts and mature pine stands. Using various assumptions about habitat suitability, we estimated that the 50-year probability of population extinction is at least 5% or may be much higher if juvenile survivorship is low. We believe, however, that modest changes in the management plan might greatly increase the sparrow population and presumably decrease the probability of extinction. Our results suggest that management plans focusing on one or a few endangered species may potentially threaten other species of management concern. Spatially explicit population models are a useful tool in designing modifications of management plans that can reduce the impact on nontarget species of management concern.     

Effects of Clear-Cut Harvesting on Boreal Ground-Beetle Assemblages (Coleoptera: Carabidae) in Western Canada

We compared pitfall catches from four types of mature lodgepole pine—white spruce forest with those from five age classes of young forest regenerating subsequent to clear-cutting. Ground beetles were most abundant in the youngest sites (1–2 years since cutting) and in the mature stands on moist soil. Species richness was higher in regenerating sites than in mature forest. Cluster analysis grouped the ground-beetle fauna according to forest age and forest type, suggesting that there is a general pattern of recovery after logging. Responses of common species to forest cutting fell into three groups: (1) forest generalists (2 species) were not dramatically affected, (2) species of open habitat (27 species) appeared and/or increased in abundance, and (3) mature forest species (10 species) disappeared or decreased in abundance. Populations of many mature forest species appear to recover following logging, but several specialists did not recolonize even the oldest regenerating stands. Furthermore, fragmentation and creation of large areas of relatively homogeneous young forest stages through logging may have detrimental long-term effects even on the more abundant forest generalists. We must better understand subtle variations in habitat in order to maintain invertebrate diversity while harvesting the boreal forest.     

The evolution of non-maternal caretaking among anthropoid primates: do helpers help?

Non-maternal infant care among nonhuman primates has frequently been investigated from the perspective of the caretaker. Here we examine whether allocaretaking behavior provides direct reproductive benefits to mothers. Comparative analyses that control for the effects of allometry and phylogeny reveal that allocaretaking behavior correlates with relatively fast infant growth and reproduction, but is not associated with the production of large infants. These results are consistent with those from studies of other taxa; primate helpers appear to increase the reproductive success of female breeders. In addition, our findings contrast with those derived from traditional allometric analyses and underscore the importance of controlling for the potentially confounding effects of phylogeny in comparative analyses. Received: 28 May 1996 / Accepted after revision: 16 November 1996     

Regulation of glycolytic enzymes in the marine invertebrateHalicryptus spinulosus (Priapulida) during environmental anoxia and exposure to hydrogen sulfide

A particularly strong reduction of metabolic activity is a precondition for long-term survival ofHalicryptus spinulosus von Siebold under anoxic habitat conditions because of its relatively low fuel reserves (mainly glycogen). The present study analyses the mechanism of this metabolic slow-down. For this purpose the effects of environmental anoxia and exposure to hydrogen sulfide on the activity and selected kinetic properties of glycolytic enzymes [glycogen phosphorylase (GP), pyruvate kinase (PK)] and the concentrations of fructose-2,6-bisphosphate in the body wall ofH. spinulosus were analysed. Anoxia and hydrogen sulfide exposure stimulated modifications of the properties of the enzymes, in both cases due to probable covalent modification of the enzyme proteins. Under both conditions phosphorylase activity was depressed by about 1/3, the result of changes in the percentage of enzyme in the activea-form as well as the total amount of enzyme activity expressed (a +b). Effects of anoxia on the properties of pyruvate kinase included reducedV _max , decreasedS _0.5 for phospho-enolpyruvate, changes inK _a for fructose-1,6-bisphosphate (an initial decrease was followed by a later increase). TheI ₅₀ forL-alanine of PK was extremely reduced under anoxia and showed an even greater sensitivity to the presence of hydrogen sulfide. Anoxia stimulated a slight reduction in the content of fructose-2,6-bisphosphate, whereas exposure to hydrogen sulfide caused a dramatic decrease of this allosteric activator of phos-phofructokinase. The study gives evidence that mechanisms of glycolytic rate depression are conserved within a wide variety of vertebrate and invertebrate phyla. With two exceptions (fructose-2,6-bisphosphate levels and alanine inhibition of PK) the responses to hydrogen sulfide were the same as those to anoxia, suggesting that at a metabolic level, the consequences of each stress on energy metabolism are similar.     

Current versus future reproduction: an experimental test of parental investment decisions using nest desertion by mallards (<Emphasis Type="Italic">Anas platyrhynchos</Emphasis>)

Past investment in offspring may be important in determining a parent's ability to reproduce in the future and, hence, should affect the relative value of current offspring. However, there have been surprisingly few clear tests of whether animals actually adjust parental care in response to diminished opportunities for future reproduction. We modified the experimental protocol of Sargent and Gross [Behav Ecol Sociobiol (1985) 17:43–45] to examine offspring desertion by mallards ( Anas platyrhynchos), and decoupled the influence of past investment from expected current benefits by controlling for the effect of offspring age on clutch value. Using 9 years of nest mortality data, we accounted for the increasing prospects of egg survival with clutch age by calculating clutch sizes throughout incubation with equivalent expected benefits. Applying this approach, we experimentally reduced 203 clutches at two different incubation stages such that they had equivalent expected benefits but differed in the amount of past investment. Nest desertion rates did not differ between early- and late-incubated clutches that had equivalent expected benefits. Rather, the probability of desertion increased with the severity of the clutch reduction treatment. These results suggest that female mallards adjust parental care according to the expected benefits of current offspring, rather than to diminished prospects for future reproduction due to past investment. We further examined whether females assessed expected benefits on the basis of clutch size alone or clutch size adjusted for the age of the clutch. Using Akaike's Information Criterion, the most parsimonious model to explain the probability of deserting an experimentally reduced clutch included both the proportion of the clutch remaining and clutch age. Thus, female mallards appear to fine-tune their level of parental care not only according to the relative number of offspring in the clutch, but also to the increased prospects for offspring survival as they age.