A Source of Terrestrial Organic Carbon to Investigate the Browning of Aquatic Ecosystems

There is growing evidence that terrestrial ecosystems are exporting more dissolved organic carbon (DOC) to aquatic ecosystems than they did just a few decades ago. This “browning” phenomenon will alter the chemistry, physics, and biology of inland water bodies in complex and difficult-to-predict ways. Experiments provide an opportunity to elucidate how browning will affect the stability and functioning of aquatic ecosystems. However, it is challenging to obtain sources of DOC that can be used for manipulations at ecologically relevant scales. In this study, we evaluated a commercially available source of humic substances (“Super Hume”) as an analog for natural sources of terrestrial DOC. Based on chemical characterizations, comparative surveys, and whole-ecosystem manipulations, we found that the physical and chemical properties of Super Hume are similar to those of natural DOC in aquatic and terrestrial ecosystems. For example, Super Hume attenuated solar radiation in ways that will not only influence the physiology of aquatic taxa but also the metabolism of entire ecosystems. Based on its chemical properties (high lignin content, high quinone content, and low C:N and C:P ratios), Super Hume is a fairly recalcitrant, low-quality resource for aquatic consumers. Nevertheless, we demonstrate that Super Hume can subsidize aquatic food webs through 1) the uptake of dissolved organic constituents by microorganisms, and 2) the consumption of particulate fractions by larger organisms (i.e., Daphnia). After discussing some of the caveats of Super Hume, we conclude that commercial sources of humic substances can be used to help address pressing ecological questions concerning the increased export of terrestrial DOC to aquatic ecosystems.     

Fitness components and ecological risk of transgenic release: a model using Japanese medaka (Oryzias latipes)

Any release of transgenic organisms into nature is a concern because ecological relationships between genetically engineered organisms and other organisms (including their wild-type conspecifics) are unknown. To address this concern, we developed a method to evaluate risk in which we input estimates of fitness parameters from a founder population into a recurrence model to predict changes in transgene frequency after a simulated transgenic release. With this method, we grouped various aspects of an organism's life cycle into six net fitness components: juvenile viability, adult viability, age at sexual maturity, female fecundity, male fertility, and mating advantage. We estimated these components for wild-type and transgenic individuals using the fish, Japanese medaka (Oryzias latipes). We generalized our model's predictions using various combinations of fitness component values in addition to our experimentally derived estimates. Our model predicted that, for a wide range of parameter values, transgenes could spread in populations despite high juvenile viability costs if transgenes also have sufficiently high positive effects on other fitness components. Sensitivity analyses indicated that transgene effects on age at sexual maturity should have the greatest impact on transgene frequency, followed by juvenile viability, mating advantage, female fecundity, and male fertility, with changes in adult viability, resulting in the least impact.     

Assessment of possible ecological risks and hazards of transgenic fish with implications for other sexually reproducing organisms

Transgenic technology is developing rapidly; however, consumers and environmentalists remain wary of its safety for use in agriculture. Research is needed to ensure the safe use of transgenic technology and thus increase consumer confidence. This goal is best accomplished by using a thorough, unbiased examination of risks associated with agricultural biotechnology. In this paper, we review discussion on risk and extend our approach to predict risk. We also distinguish between the risk and hazard of transgenic organisms in natural environments. We define transgene risk as the probability a transgene will spread into natural conspecific populations and define hazard as the probability of species extinction, displacement, or ecosystem disruption given that the transgene has spread. Our methods primarily address risk relative to two types of hazards: extinction which has a high hazard, and invasion which has an unknown level of hazard, similar to that of an introduced exotic species. Our method of risk assessment is unique in that we concentrate on the six major fitness components of an organism's life cycle to determine if transgenic individuals differ in survival or reproductive capacity from wild type. Our approach then combines estimates of the net fitness parameters into a mathematical model to determine the fate of the transgene and the affected wild population. We also review aspects of fish ecology and behavior that contribute to risk and examine combinations of net fitness parameters which can lead to invasion and extinction hazards. We describe three new ways that a transgene could result in an extinction hazard: (1) when the transgene increases male mating success but reduces daily adult viability, (2) when the transgene increases adult viability but reduces male fertility, and (3) when the transgene increases both male mating success and adult viability but reduces male fertility. The last scenario is predicted to cause rapid extinction, thus it poses an extreme risk. Although we limit our discussion to aquacultural applications, our methods can easily be adapted to other sexually reproducing organisms with suitable adjustments of terminology.     

Complex interactions among fish, snails and macrophytes: implications for biological control of an invasive snail

The golden apple snail (Pomacea canaliculata), a native of freshwater wetlands of South America, has invaded many Asian countries and grazed heavily in agricultural and wild areas. Common carp (Cyprinus carpio) has been proposed as a biological control agent against this snail, but little is known about its impact on non-target aquatic plants and animals. In a 8-week enclosure experiment, we quantified the impact of common carp on three species of aquatic macrophytes and nine species of snails, including the apple snail, in a shallow pond. The results showed that the apple snail or carp alone significantly reduced the plant biomass, although the apple snail had a stronger overall herbivorous effect than the carp. The carp completely removed juvenile apple snails, but had only a weak predatory effect on larger apple snails and no effect on the adults’ oviposition frequency. Furthermore, the carp significantly reduced the populations of most species of other snails that occurred naturally in the pond. Our results thus indicate that common carp can be an effective biological control agent against the invasive apple snail, but caution should be taken about its potential to reduce wetland floral and faunal diversity.     

Molecular Characterization of the Nonphotosynthetic Partner Bacterium in the Consortium “Chlorochromatium aggregatum”

Phototrophic consortia represent valuable model systems for the study of signal transduction and coevolution between different bacteria. The phototrophic consortium “Chlorochromatium aggregatum” consists of a colorless central rod-shaped bacterium surrounded by about 20 green-pigmented epibionts. Although the epibiont was identified as a member of the green sulfur bacteria, and recently isolated and characterized in pure culture, the central colorless bacterium has been identified as a member of the β-Proteobacteria but so far could not be characterized further. In the present study, “C. aggregatum” was enriched chemotactically, and the 16S rRNA gene sequence of the central bacterium was elucidated. Based on the sequence information, fluorescence in situ hybridization probes targeting four different regions of the 16S rRNA were designed and shown to hybridize exclusively to cells of the central bacterium. Phylogenetic analyses of the 1,437-bp-long sequence revealed that the central bacterium of “C. aggregatum” represents a so far isolated phylogenetic lineage related to Rhodoferax spp., Polaromonas vacuolata, and Variovorax paradoxus within the family Comamonadaceae. The majority of relatives of this lineage are not yet cultured and were found in low-temperature aquatic environments or aquatic environments containing xenobiotica or hydrocarbons. In CsCl-bisbenzimidazole equilibrium density gradients, genomic DNA of the central bacterium of “Chlorochromatium aggregatum” formed a distinct band which could be detected by quantitative PCR using specific primers. Using this method, the G+C content of the central bacterium was determined to be 55.6 mol%.     

Social associations in common carp (Cyprinus carpio): Insights from induced feeding aggregations for targeted management strategies

Heterogeneity in social interactions can have important consequences for the spread of information and diseases and consequently conservation and invasive species management. Common carp (Cyprinus carpio) are a highly social, ubiquitous, and invasive freshwater fish. Management strategies targeting foraging carp may be ideal because laboratory studies have suggested that carp can learn, have individual personalities, a unique diet, and often form large social groups. To examine social feeding behaviors of wild carp, we injected 344 carp with passive integrated transponder (PIT) tags and continuously monitored their feeding behaviors at multiple sites in a natural lake in Minnesota, USA. The high‐resolution, spatio‐temporal data were analyzed using a Gaussian mixture model (GMM). Based on these associations, we analyzed group size, feeding bout duration, and the heterogeneity and connectivity of carp social networks at foraging sites. Wild carp responded quickly to bait, forming aggregations most active from dusk to dawn. During the 2020 baiting period (20 days), 133 unique carp were detected 616,593 times. There was some evidence that feeding at multiple sites was constrained by basin geography, but not distance alone. GMM results suggested that feeding bouts were short, with frequent turnover of small groups. Individual foraging behavior was highly heterogeneous with Gini coefficients of 0.79 in 2020 and 0.66 in 2019. “Superfeeders”—those contributing to 80% of total cumulative detections (top 18% and top 29% of foragers in 2020 and 2019 respectively)—were more likely to be detected earlier at feeding stations, had larger body sizes, and had higher network measures of degree, weighted degree, and betweenness than non‐superfeeders. Overall, our results indicate that wild carp foraging is social, easily induced by bait, dominated by large‐bodied individuals, and potentially predictable, which suggests social behaviors could be leveraged in management of carp, one of the world''s most recognizable and invasive fish.     

Animal‐borne video systems provide insight into the reproductive behavior of the Asian black bear

Previous studies on the mating system of the Asian black bear (Ursus thibetanus) have been limited to observations of captive populations and estimations of multiple paternities. Hence, the mating system of wild bears remains poorly understood. Animal‐borne camera systems (i.e., cameras mounted on animals) provide novel tools to study the behavior of elusive animals. Here, we used an animal‐borne video system to record the activities of wild bears during the mating season. Video camera collars were attached to four adult Asian black bears (male “A” and “B,” and female “A” and “B”) captured in Tokyo, central Japan, in May and June 2018. The collars were retrieved in July 2018, after which the video data were downloaded and analyzed in terms of bear activity and mating behavior. All the bears were found to interact with other uniquely identifiable bears for some of the time (range 9–22 days) during the deployment period (range 36–45 days), and multiple mating in males was documented. Both males and females exhibited different behaviors on social days (i.e., days when the bear interacted with conspecifics) compared with solitary days (i.e., days with no observed interactions with conspecifics). Compared with solitary days, the bears spent a lower proportion of time on foraging activities and higher proportion of time on resting activities on social days. Our results suggest that Asian black bears have a polygamous mating system, as both sexes consort and potentially mate with multiple partners during a given mating season. Furthermore, bears appeared to reduce their foraging activities on social days and engaged more in social interactions.     

Environmental Noise,Genetic Diversity and the Evolution of Evolvability and Robustness in Model Gene Networks

The ability of organisms to adapt and persist in the face of environmental change is accepted as a fundamental feature of natural systems. More contentious is whether the capacity of organisms to adapt (or “evolvability”) can itself evolve and the mechanisms underlying such responses. Using model gene networks, I provide evidence that evolvability emerges more readily when populations experience positively autocorrelated environmental noise (red noise) compared to populations in stable or randomly varying (white noise) environments. Evolvability was correlated with increasing genetic robustness to effects on network viability and decreasing robustness to effects on phenotypic expression; populations whose networks displayed greater viability robustness and lower phenotypic robustness produced more additive genetic variation and adapted more rapidly in novel environments. Patterns of selection for robustness varied antagonistically with epistatic effects of mutations on viability and phenotypic expression, suggesting that trade-offs between these properties may constrain their evolutionary responses. Evolution of evolvability and robustness was stronger in sexual populations compared to asexual populations indicating that enhanced genetic variation under fluctuating selection combined with recombination load is a primary driver of the emergence of evolvability. These results provide insight into the mechanisms potentially underlying rapid adaptation as well as the environmental conditions that drive the evolution of genetic interactions.     

Contrasting Patterns of Larval Mortality in Two Sympatric Riverine Fish Species: A Test of the Critical Period Hypothesis

Understanding the causal mechanisms that determine recruitment success is critical to the effective conservation of wild fish populations. Although recruitment strength is likely determined during early life when mortality is greatest, few studies have documented age-specific mortality rates for fish during this period. We investigated age-specific mortality of individual cohorts of two species of riverine fish from yolksac larvae to juveniles, assaying for the presence of a “critical period”: A time when mortality is unusually high. Early life stages of carp gudgeons (Hypseleotris spp.) and unspecked hardyhead (Craterocephalus stercusmuscarum fulvus)—two fishes that differ in fecundity, egg size and overlap between endogenous and exogenous feeding—were collected every second day for four months. We fitted survivorship curves to 22 carp gudgeon and 15 unspecked hardyhead four-day cohorts and tested several mortality functions. Mortality rates declined with age for carp gudgeon, with mean instantaneous mortality rates (-Z) ranging from 1.40–0.03. In contrast, mortality rates for unspecked hardyhead were constant across the larval period, with a mean -Z of 0.15. There was strong evidence of a critical period for carp gudgeon larvae from hatch until 6 days old, and no evidence of a critical period for unspecked hardyhead. Total larval mortality for carp gudgeon and unspecked hardyhead up to 24 days of age was estimated to be 97.8 and 94.3%, respectively. We hypothesise that life history strategy may play an important role in shaping overall mortality and the pattern of mortality during early life in these two fishes.     

Aspects of Embryonic and Larval Development in Bighead Carp Hypophthalmichthys nobilis and Silver Carp Hypophthalmichthys molitrix

As bighead carp Hypophthalmichthys nobilis and silver carp H . molitrix (the bigheaded carps) are poised to enter the Laurentian Great Lakes and potentially damage the region’s economically important fishery, information on developmental rates and behaviors of carps is critical to assessing their ability to establish sustainable populations within the Great Lakes basin. In laboratory experiments, the embryonic and larval developmental rates, size, and behaviors of bigheaded carp were tracked at two temperature treatments, one “cold” and one “warm”. Developmental rates were computed using previously described stages of development and the cumulative thermal unit method. Both species have similar thermal requirements, with a minimum developmental temperature for embryonic stages of 12.1° C for silver carp and 12.9° C for bighead carp, and 13.3° C for silver carp larval stages and 13.4° C for bighead carp larval stages. Egg size differed among species and temperature treatments, as egg size was larger in bighead carp, and “warm" temperature treatments. The larvae started robust upwards vertical swimming immediately after hatching, interspersed with intervals of sinking. Vertical swimming tubes were used to measure water column distribution, and ascent and descent rates of vertically swimming fish. Water column distribution and ascent and descent rates changed with ontogeny. Water column distribution also showed some diel periodicity. Developmental rates, size, and behaviors contribute to the drift distance needed to fulfill the early life history requirements of bigheaded carps and can be used in conjunction with transport information to assess invasibility of a river.     

Phenotypic Plasticity in Response to the Social Environment: Effects of Density and Sex Ratio on Mating Behaviour Following Ecotype Divergence

The ability to express phenotypically plastic responses to environmental cues might be adaptive in changing environments. We studied phenotypic plasticity in mating behaviour as a response to population density and adult sex ratio in a freshwater isopod (Asellus aquaticus). A. aquaticus has recently diverged into two distinct ecotypes, inhabiting different lake habitats (reed Phragmites australis and stonewort Chara tomentosa, respectively). In field surveys, we found that these habitats differ markedly in isopod population densities and adult sex ratios. These spatially and temporally demographic differences are likely to affect mating behaviour. We performed behavioural experiments using animals from both the ancestral ecotype (“reed” isopods) and from the novel ecotype (“stonewort” isopods) population. We found that neither ecotype adjusted their behaviour in response to population density. However, the reed ecotype had a higher intrinsic mating propensity across densities. In contrast to the effects of density, we found ecotype differences in plasticity in response to sex ratio. The stonewort ecotype show pronounced phenotypic plasticity in mating propensity to adult sex ratio, whereas the reed ecotype showed a more canalised behaviour with respect to this demographic factor. We suggest that the lower overall mating propensity and the phenotypic plasticity in response to sex ratio have evolved in the novel stonewort ecotype following invasion of the novel habitat. Plasticity in mating behaviour may in turn have effects on the direction and intensity of sexual selection in the stonewort habitat, which may fuel further ecotype divergence.     

Sexuality and Genetic Identity in the Agaricus Section Arvenses

Twelve wild collections and one commercial strain were used to characterize breeding systems and to develop molecular identities in the Arvenses section of the genus Agaricus, which includes the “horse mushroom” A. arvensis. Two morphotypes were identified based on macro- and micromorphological features. However, not all collections could be delimited by conventional taxonomic characters. Sequencing of the small subunit intergenic spacer (ITS) region (368 to 370 bp) of the rRNA genes clearly resolved the 13 collections into two clusters consistent with the identified morphotypes. Single-spore progenies and mating type testers were established and used to test intra- and interstock compatibility. The two compatibility groups identified were consistent with ITS clusters. Compatibility group I stocks readily interbred within the constraints of a unifactorial heterothallic system with a multiallelic mating type factor. Compatibility group II had a more restricted breeding pattern, and interactions were difficult to predict on the basis of mating type. Morphological data, ITS sequences, and the ability to interbreed suggest that these collections are part of a complex of interrelated species. Single-spore, homokaryotic isolates from both compatibility groups were able to fruit in compost culture, and two of the collections may represent natural homokaryotic fruiting. We conclude that species from the section Arvenses have versatile unifactorial heterothallic life cycles that permit both interbreeding and homokaryotic fruiting.     

The rates of shoot and root growth in intact plants of pea mutants in leaf morphology

Isogenic lines of pea (Pisum sativum L.) with the genetically determined changes in leaf morphology, afila (af) and tendril-less (tl), were used to study the relationship between shoot and root growth rates. The time-course of shoot and root growth was followed during the pre-floral period in the intact plants grown under similar conditions. The af mutation produced afila leaves without leaflets, whereas in the case of the tl mutations, tendrils were substituted with leaflets, and acacia-like leaves were developed. Due to the changes in leaf morphology caused by these mutations, pea genotypes differed in leaf area: starting from day 7, the leaf area was lower in the af plants and larger in the tl plants as compared to the wild-type plants. Such divergence was amplified in the course of plant development and reached its maximum immediately before the transition to flowering. Plants of isogenic lines did not notably differ in stem surface areas. In spite of significant difference in total leaf area, the wild type and tl plants did not differ in leaf dry weight. Starting from leaf 9, the af plants lagged behind two leaflet-bearing genotypes (wild type and tl) in leaf dry weight, whereas stem dry weight was similar in the wild type and tl forms and slightly lower in the af plants. Root dry weights were practically similar in the wild type and tl plants until flowering. The reduction of leaf area in the af plants drastically reduced root dry weight. In other words, the latter index was related to the total weight and total area of leaves and stems. The correlation analysis demonstrated an extremely low relationship between leaf and stem area and dry weight and those of roots early in plant development (when plants develop five to seven leaves). Later, immediately before flowering (nine to eleven leaves), root weight was positively related to leaf weight and area; however, stem area and root weight did not correlate. Thus, in three genotypes (wild type, af, and tl), at the end of their vegetative growth phase, leaf and root biomass accumulated in proportion, independently of leaf area expansion.     

Biochemical characterisation of the clamp/clamp loader proteins from the euryarchaeon Archaeoglobus fulgidus

Replicative polymerases of eukaryotes, prokaryotes and archaea obtain processivity using ring-shaped DNA sliding clamps that are loaded onto DNA by clamp loaders [replication factor C (RFC) in eukaryotes]. In this study, we cloned the two genes for the subunits of the RFC homologue of the euryarchaeon Archaeoglobus fulgidus. The proteins were expressed and purified from Escherichia coli both individually and as a complex. The afRFC subunits form a heteropentameric complex consisting of one copy of the large subunit and four copies of the small subunits. To analyse the functionality of afRFC, we also expressed the A.fulgidus PCNA homologue and a type B polymerase (PolB1) in E.coli. In primer extension assays, afRFC stimulated the processivity of afPolB1 in afPCNA-dependent reactions. Although the afRFC complex showed significant DNA-dependent ATPase activity, which could be further stimulated by afPCNA, neither of the isolated afRFC subunits showed this activity. However, both the large and small afRFC subunits showed interaction with afPCNA. Furthermore, we demonstrate that ATP binding, but not hydrolysis, is needed to stimulate interactions of the afRFC complex with afPCNA and DNA.     

Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere

It is now indisputable that plastics are ubiquitous and problematic in ecosystems globally. Many suggestions have been made about the role that biofilms colonizing plastics in the environment—termed the “Plastisphere”—may play in the transportation and ecological impact of these plastics. By collecting and re-analyzing all raw 16S rRNA gene sequencing and metadata from 2,229 samples within 35 studies, we have performed the first meta-analysis of the Plastisphere in marine, freshwater, other aquatic (e.g., brackish or aquaculture) and terrestrial environments. We show that random forest models can be trained to differentiate between groupings of environmental factors as well as aspects of study design, but—crucially—also between plastics when compared with control biofilms and between different plastic types and community successional stages. Our meta-analysis confirms that potentially biodegrading Plastisphere members, the hydrocarbonoclastic Oceanospirillales and Alteromonadales are consistently more abundant in plastic than control biofilm samples across multiple studies and environments. This indicates the predilection of these organisms for plastics and confirms the urgent need for their ability to biodegrade plastics to be comprehensively tested. We also identified key knowledge gaps that should be addressed by future studies.Subject terms: Microbial ecology, Soil microbiology, Water microbiology, Microbial ecology, Microbiome     

Decay of TRPV3 as the genomic trace of epidermal structure changes in the land‐to‐sea transition of mammals

The epidermis plays an indispensable barrier function in animals. Some species have evolved unique epidermal structures to adapt to different environments. Aquatic and semi‐aquatic mammals (cetaceans, manatees, and hippopotamus) are good models to study the evolution of epidermal structures because of their exceptionally thickened stratum spinosum, the lack of stratum granulosum, and the parakeratotic stratum corneum. This study aimed to analyze an upstream regulatory gene transient receptor potential cation channel, subfamily V, member 3 (TRPV3) of epidermal differentiation so as to explore the association between TRPV3 evolution and epidermal changes in mammals. Inactivating mutations were detected in almost all the aquatic cetaceans and several terrestrial mammals. Relaxed selective pressure was examined in the cetacean lineages with inactivated TRPV3, which might contribute to its exceptionally thickened stratum spinosum as the significant thickening of stratum spinosum in TRPV3 knock‐out mouse. However, functional TRPV3 may exist in several terrestrial mammals due to their strong purifying selection, although they have “inactivating mutations.” Further, for intact sequences, relaxed selective constraints on the TRPV3 gene were also detected in aquatic cetaceans, manatees, and semi‐aquatic hippopotamus. However, they had intact TRPV3, suggesting that the accumulation of inactivating mutations might have lagged behind the relaxed selective pressure. The results of this study revealed the decay of TRPV3 being the genomic trace of epidermal development in aquatic and semi‐aquatic mammals. They provided insights into convergently evolutionary changes of epidermal structures during the transition from the terrestrial to the aquatic environment.