Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia) reveal new threats

Worldwide coral reef decline appears to be accompanied by an increase in the spread of hard coral diseases. However, whether this is the result of increased direct and indirect human disturbances and/or an increase in natural stresses remains poorly understood. The provision of baseline surveys for monitoring coral health status lays the foundations to assess the effects of any such anthropogenic and/or natural effects on reefs. Therefore, the objectives of this present study were to provide a coral health baseline in a poorly studied area, and to investigate possible correlations between coral health and the level of anthropogenic and natural disturbances. During the survey period, we recorded 20 different types of coral diseases and other compromised health statuses. The most abundant were cases of coral bleaching, followed by skeletal deformations caused by pyrgomatid barnacles, damage caused by fish bites, general pigmentation response and galls caused by cryptochirid crabs. Instances of colonies affected by skeletal eroding bands, and sedimentation damage increased in correlation to the level of bio-chemical disturbance and/or proximity to villages. Moreover, galls caused by cryptochirid crabs appeared more abundant at sites affected by blast fishing and close to a newly opened metal mine. Interestingly, in the investigated area the percentage of corals showing signs of ‘common’ diseases such as black band disease, brown band disease, white syndrome and skeletal eroding band disease were relatively low. Nevertheless, the relatively high occurrence of less common signs of compromised coral-related reef health, including the aggressive overgrowth by sponges, deserves further investigation. Although diseases appear relatively low at the current time, this area may be at the tipping point and an increase in activities such as mining may irredeemably compromise reef health.This research was partially funded by Coral Eye, which hosted FF and covered all field expenses. The non-profit organization Reef Check Italia Onlus sustained the cost for open source publication. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Optimality of extracellular enzyme production and activity in dynamic flux balance modeling

In microbial communities, many vital metabolic functions, including the degradation of cellulose, proteins and other complex macromolecules, are carried out by costly, extracellularly secreted enzymes. While significant effort has been dedicated to analyzing genome-scale metabolic networks for individual microbes and communities, little is known about the interplay between global allocation of metabolic resources in the cell and extracellular enzyme secretion and activity. Here we introduce a method for modeling the secretion and catalytic functions of extracellular enzymes using dynamic flux balance analysis. This new addition, implemented within COMETS (Computation Of Microbial Ecosystems in Time and Space), simulates the costly production and secretion of enzymes and their diffusion and activity throughout the environment, independent of the producing organism. After tuning our model based on data for a Saccharomyces cerevisiae strain engineered to produce exogenous cellulases, we explored the dynamics of the system at different cellulose concentrations and enzyme production rates. We found that there are distinct rates of constitutive enzyme secretion which maximize either growth rate or biomass yield. These optimal rates are strongly dependent on enzyme kinetic properties and environmental conditions, including the amount of cellulose substrate available. Our framework will facilitate the development of more realistic simulations of microbial community dynamics within environments rich in complex macromolecules, with applications in the study of soil and plant-associated ecosystems, and other natural and engineered microbiomes.https://www.biorxiv.org/content/10.1101/2021.11.01.466736v1First author draf

Visual Sensory Signals Dominate Tactile Cues during Docked Feeding in Hummingbirds

Animals living in and interacting with natural environments must monitor and respond to changing conditions and unpredictable situations. Using information from multiple sensory systems allows them to modify their behavior in response to their dynamic environment but also creates the challenge of integrating different, and potentially contradictory, sources of information for behavior control. Understanding how multiple information streams are integrated to produce flexible and reliable behavior is key to understanding how behavior is controlled in natural settings. Natural settings are rarely still, which challenges animals that require precise body position control, like hummingbirds, which hover while feeding from flowers. Tactile feedback, available only once the hummingbird is docked at the flower, could provide additional information to help maintain its position at the flower. To investigate the role of tactile information for hovering control during feeding, we first asked whether hummingbirds physically interact with a feeder once docked. We quantified physical interactions between docked hummingbirds and a feeder placed in front of a stationary background pattern. Force sensors on the feeder measured a complex time course of loading that reflects the wingbeat frequency and bill movement of feeding hummingbirds, and suggests that they sometimes push against the feeder with their bill. Next, we asked whether the measured tactile interactions were used by feeding hummingbirds to maintain position relative to the feeder. We created two experimental scenarios—one in which the feeder was stationary and the visual background moved and the other where the feeder moved laterally in front of a white background. When the visual background pattern moved, docked hummingbirds pushed significantly harder in the direction of horizontal visual motion. When the feeder moved, and the background was stationary, hummingbirds generated aerodynamic force in the opposite direction of the feeder motion. These results suggest that docked hummingbirds are using visual information about the environment to maintain body position and orientation, and not actively tracking the motion of the feeder. The absence of flower tracking behavior in hummingbirds contrasts with the behavior of hawkmoths, and provides evidence that they rely primarily on the visual background rather than flower-based cues while feeding

Hemisystems of small flock generalized quadrangles

In this paper, we describe a complete computer classification of the hemisystems in the two known flock generalized quadrangles of order $(5^2,5)$ and give numerous further examples of hemisystems in all the known flock generalized quadrangles of order $(s^2,s)$ for $s \le 11$. By analysing the computational data, we identify two possible new infinite families of hemisystems in the classical generalized quadrangle $H(3,q^2)$.Comment: slight revisions made following referee's reports, and included raw dat

Adaptive Diversification in Genes That Regulate Resource Use in Escherichia coli

While there has been much recent focus on the ecological causes of adaptive diversification, we know less about the genetic nature of the trade-offs in resource use that create and maintain stable, diversified ecotypes. Here we show how a regulatory genetic change can contribute to sympatric diversification caused by differential resource use and maintained by negative frequency-dependent selection in Escherichia coli. During adaptation to sequential use of glucose and acetate, these bacteria differentiate into two ecotypes that differ in their growth profiles. The “slow-switcher” exhibits a long lag when switching to growth on acetate after depletion of glucose, whereas the “fast-switcher” exhibits a short switching lag. We show that the short switching time in the fast-switcher is associated with a failure to down-regulate potentially costly acetate metabolism during growth on glucose. While growing on glucose, the fast-switcher expresses malate synthase A (aceB), a critical gene for acetate metabolism that fails to be properly down-regulated because of a transposon insertion in one of its regulators. Swapping the mutant regulatory allele with the ancestral allele indicated that the transposon is in part responsible for the observed differentiation between ecological types. Our results provide a rare example of a mechanistic integration of diversifying processes at the genetic, physiological, and ecological levels

Four Linked Genes Participate in Controlling Sporulation Efficiency in Budding Yeast

Quantitative traits are conditioned by several genetic determinants. Since such genes influence many important complex traits in various organisms, the identification of quantitative trait loci (QTLs) is of major interest, but still encounters serious difficulties. We detected four linked genes within one QTL, which participate in controlling sporulation efficiency in Saccharomyces cerevisiae. Following the identification of single nucleotide polymorphisms by comparing the sequences of 145 genes between the parental strains SK1 and S288c, we analyzed the segregating progeny of the cross between them. Through reciprocal hemizygosity analysis, four genes, RAS2, PMS1, SWS2, and FKH2, located in a region of 60 kilobases on Chromosome 14, were found to be associated with sporulation efficiency. Three of the four “high” sporulation alleles are derived from the “low” sporulating strain. Two of these sporulation-related genes were verified through allele replacements. For RAS2, the causative variation was suggested to be a single nucleotide difference in the upstream region of the gene. This quantitative trait nucleotide accounts for sporulation variability among a set of ten closely related winery yeast strains. Our results provide a detailed view of genetic complexity in one “QTL region” that controls a quantitative trait and reports a single nucleotide polymorphism-trait association in wild strains. Moreover, these findings have implications on QTL identification in higher eukaryotes