Rubble fields shape planktonic protist communities in Indonesia at a local scale

The Coral Triangle encompasses nearly 30% of the world's coral reefs and is widely considered the epicenter of marine biodiversity. Destructive fishing practices and natural disturbances common to this region damage reefs leaving behind fields of coral rubble. While the impacts of disturbances in these ecosystems are well documented on metazoans, we have a poor understanding of their impact on microbial communities at the base of the food web. We use metabarcoding to characterize protist community composition in sites of varying fisheries management schemes and benthic profiles across the island of Lombok, Indonesia. Our study shows that rubble coverage and net primary productivity are the strongest explainers of variation in protist communities across Lombok. More specifically, rubble fields are characterized by increases in small heterotrophic protists, including ciliates and cercozoans. In addition to shifts in heterotrophic protist communities, we also observed increases in diatom relative abundance in rubble fields, which corresponded to sites with higher net primary productivity. These results are the first to characterize protist communities in tropical marine rubble fields and provide insight on environmental factors potentially driving these shifts on a local scale.     

A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist

The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrion-encoded RM system can function as a toxin–antitoxin selfish element, and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.

This study reveals that a functional type II restriction modification system of flavobacterial ancestry has been horizontally transferred into the mitochondrion of a marine protist and is capable of encoding potent function, perhaps allowing it to play a role in inter-organellar warfare or protection against further integration of foreign DNA.     

Trophic relationships between planktonic bacteria,heterotrophic nanoflagellates and viruses in a mesoeutrophic reservoir

The abundance, biomass, and production (Р _В) of bacrerioplankton; the taxonomic composition, abundance, biomass of heterotrophic nanoflagellates (HNF) and the rate of consumption of bacteria by HNFs; and the abundance of virioplankton, frequency of visibly infected bacterial cells, virus-induced mortality of bacterioplankton, and viral production were estimated in the mesoeutrophic Rybinsk Reservoir. The rate of bacterial mortality due to viral lysis (7.8–34.1%, on average 17.2 ± 2.0% of daily Р _В) was lower than the consumption of bacteria by the HNF community (15.4–61.3%, on average 32.0 ± 4.2% of daily Р _В). While consuming bacteria, HNFs simultaneously absorbed a significant number of viruses residing on the surface and inside the bacterial cells.     

Vertical niche partitioning between cryptic sibling species of a cosmopolitan marine planktonic protist

A large portion of the surface‐ocean biomass is represented by microscopic unicellular plankton. These organisms are functionally and morphologically diverse, but it remains unclear how their diversity is generated. Species of marine microplankton are widely distributed because of passive transport and lack of barriers in the ocean. How does speciation occur in a system with a seemingly unlimited dispersal potential? Recent studies using planktonic foraminifera as a model showed that even among the cryptic genetic diversity within morphological species, many genetic types are cosmopolitan, lending limited support for speciation by geographical isolation. Here we show that the current two‐dimensional view on the biogeography and potential speciation mechanisms in the microplankton may be misleading. By depth‐stratified sampling, we present evidence that sibling genetic types in a cosmopolitan species of marine microplankton, the planktonic foraminifer Hastigerina pelagica, are consistently separated by depth throughout their global range. Such strong separation between genetically closely related and morphologically inseparable genetic types indicates that niche partitioning in marine heterotrophic microplankton can be maintained in the vertical dimension on a global scale. These observations indicate that speciation along depth (depth‐parapatric speciation) can occur in vertically structured microplankton populations, facilitating diversification without the need for spatial isolation.     

Global abundance of planktonic heterotrophic protists in the deep ocean

The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their abundance and biomass in deepwater column samples from the Malaspina 2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were ubiquitously found at all depths investigated down to 4000 m. HP abundances decreased with depth, from an average of 72±19 cells ml⁻¹ in mesopelagic waters down to 11±1 cells ml⁻¹ in bathypelagic waters, whereas their total biomass decreased from 280±46 to 50±14 pg C ml⁻¹. The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen concentration. The generally good correlation with prokaryotic abundance suggested active grazing of HP on prokaryotes. On a finer scale, the prokaryote:HP abundance ratio varied at a regional scale, and sites with the highest ratios exhibited a larger contribution of fungi molecular signal. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean''s microbial food web.     

Spatial structuring and dispersal in a high density population of the California vole Microtus californicus

Space use patterns of California voles are described from intensive live-trapping data obtained during the late breeding season in a peak density year. Operational sex ratios were strongly female biased. Breeding males had mutually exclusive home ranges that overlapped the home ranges of one to several females. The average male home range was larger than the average female home range and tended to encompass female home ranges in their entirety. Breeding females had home ranges that often overlapped extensively with the home ranges of other breeding females. The degree of overlap, however, tended to be either very high or very low, indicating that groups of females may act territorially among themselves. Family groups that may include members of sequential litters formed at high density. Males on experimental removal grids had larger home ranges than males on the high density grids and some became wanderers while most females had home ranges comparable to those on the high density grids.
Dispersers onto low density grids were not a random sample of the high density population; large breeding adults and small juveniles were under-represented. No sex differences in dispersal were noted. Immigration into the high density populations was probably negligible.     

Environmentally-controlled,density-dependent secondary dispersal in a local estuarine crab population

The mechanisms driving the pelagic secondary dispersal of aquatic organisms following initial settlement to benthic habitats are poorly characterized. We examined the physical environmental (wind, diel cycle, tidal phase) and biological (ontogenetic, density-dependent) factors that contribute to the secondary dispersal of a benthic marine invertebrate, the blue crab (Callinectes sapidus) in Pamlico Sound, NC, USA. Field studies conducted in relatively large (0.05 km²) seagrass beds determined that secondary dispersal is primarily undertaken by the earliest juvenile blue crab instar stages (J1 crabs). These crabs emigrated pelagically from seagrass settlement habitats using nighttime flood tides during average wind conditions (speed ~5 m s^–1). Moreover, the secondary dispersal of J1 crabs was density-dependent and regulated by intra-cohort (J1) crab density in seagrass. Our results suggest that dispersal occurs rapidly following settlement, and promotes blue crab metapopulation persistence by redistributing juveniles from high-density settlement habitats to areas characterized by low postlarval supply. Collectively, these data indicate that blue crab secondary dispersal is an active process under behavioral control and can alter initial distribution patterns established during settlement. This study highlights the necessity of considering secondary dispersal in ecological studies to improve our understanding of population dynamics of benthic organisms.     

Direct and indirect effects of protist predation on population size structure of a bacterial strain with high phenotypic plasticity

We studied the impact of grazing and substrate supply on the size structure of a freshwater bacterial strain (Flectobacillus sp.) which showed pronounced morphological plasticity. The cell length varied from 2 to >40 microm and encompassed rods, curved cells, and long filaments. Without grazers and with a sufficient substrate supply, bacteria grew mainly in the form of medium-sized rods (4 to 7 microm), with a smaller proportion (<10%) of filamentous forms. Grazing experiments with the bacterivorous flagellate Ochromonas sp. showed that freely suspended cells of <7 microm were highly vulnerable to grazers, whereas filamentous cells were resistant to grazing and became enriched during predation. A comparison of long-term growth in carbon-limited chemostats with and without grazers revealed that strikingly different bacterial populations developed: treatments with flagellates were composed of >80% filamentous cells. These attained a biomass comparable to that of populations in chemostats without grazers, which were composed of medium-sized rods and c-shaped cells. Carbon starvation resulted in a fast decrease in cell length and a shift towards small rods, which were highly vulnerable to grazing. Dialysis bag experiments in combination with continuous cultivation revealed that filament formation was significantly enhanced even without direct contact of bacteria with bacterivores and was thus probably stimulated by grazer excretory products.     

Growth, gas vacuolation and buoyancy in a natural population of a planktonic blue-green alga

(1)The growth and development of a natural population of Anabaena circinalisis described in relation to physical and chemical conditions within a small, shallow eutrophic lake. (2)Germination of resting spores took place when the lake was destratified, in response to improving conditions of light and temperature. (3)The growth of the population was monitored for chlorophyll and nutrient content, and parallel determinations of heterocyst ratio, gas vacuole volume, turgor and buoyancy were made. (4)Growth of the population was probably limited by phosphorus deficiency. (5)Cessation of growth was marked by increases in gas vacuole volume and buoyancy. (6)Gas vacuole volume is determined primarily by the rate of increase of the alga. It is modified by turgor changes, associated with photosynthetic rates. (7)Surface blooms are the result of the redistribution of buoyant algae when turbulence currents are weak. (8)Buoyancy is increased in algae lodged at the surface.     

Spatial structure, dispersal, and management of a recovering raptor population

The recovery of the peregrine falcon (Falco peregrinus anatum) in California has taken place amid strong geographical differences in habitat quality, potentially creating a sink population in the southern coastal habitat and source populations in the northern interior and urban habitats. We analyzed long-term monitoring data to investigate the mechanisms and consequences of spatial structuring for the recovery of this set of nonstable subpopulations. Dispersal rates between habitats were asymmetric, with extremely limited dispersal out of the interior habitat and a strong tendency for birds in the southern coast to disperse to the urban habitats. We used these dispersal estimates and habitat-specific productivity rates to build a set of regional population models that describe population growth within and dispersal between each subpopulation. We tested for the existence of habitat-specific survival and territory acquisition rates by comparing model projections with the number of breeding pairs censused annually in each subpopulation. Our analyses indicate a high rate of survival for interior birds and suggest that both the interior and urban subpopulations were regulated by territory availability over the study period. The inherent spatial structure of this regional peregrine falcon population has had a considerable influence on its recovery and management.     

Puberty and dispersal in a wild primate population

This article is part of a Special Issue “Puberty and Adolescence”.     

Foundations of gregariousness: a dispersal polymorphism among the planktonic larvae of a marine invertebrate

Theory predicts that selection should favor genotypes that can vary their tendency to disperse in habitats that are spatially or temporally variable or those that remain near their carrying capacity. Although many marine habitats appear to fit these criteria, confirmed examples of dispersal polymorphism among marine invertebrates are exceedingly rare. Competent larvae of the gregarious tubeworm, Hydroides dianthus, settle specifically in response to living conspecific worms, but a small proportion of each spawn settle nonspecifically on uninhabited substrata concurrently with their gregarious siblings. Here, using a parental half-sib analysis, we show that the proportion of a spawn settling in response to uninhabited biofilm is highly heritable. When estimated as a continuous trait based on a one-way ANOVA, heritability is estimated to be 0.83 +/- 0.31. When founder production was analyzed as a threshold trait, heritability was estimated to be 0.68 +/- 0.10 based on the breeding design experiment and 0.65 +/- 0.09 based on the artificial selection experiments. Realized heritability based on the selection experiments was considerably lower, however (0.17 per generation and 0.02 cumulative). Artificial selection was ineffectual at sequentially increasing the proportion of founder larvae among inbred family lines, but after three generations of selection, the proportion of larvae settling in response to biofilm was significantly higher among inbred lines than among the field-collected parents. The obligate planktonic larval stage common among so many marine invertebrates is thought to preclude the evolution of dispersal polymorphisms in these animals. Theoretical expectations of variable dispersal may instead be realized through individual behavioral differences resulting in differential transport or settlement preference, but this possibility remains largely unexplored among marine invertebrates.     

Use of heterotrophic CO2 assimilation as a measure of metabolic activity in planktonic and sessile bacteria

We have examined whether assimilation of CO2 can be used as a measure of metabolic activity in planktonic and sessile heterotrophic bacteria. CO2 assimilation by environmental samples and pure cultures of heterotrophic bacteria was studied using 14CO2 and 13CO2 as tracers. Heterotrophic growth on complex organic substrates resulted in assimilation of CO2 into cell biomass by activated sludge, drinking water biofilm, and pure cultures of Escherichia coli ATCC 25922, Es. coli ATCC 13706, Rhodococcus ruber, Burkholderia sp., Bacillus circulans, Pseudomonas putida, Pseudomonas stutzeri, and Pseudomonas aeruginosa. Analysis of 13C-labelled phospholipid fatty acids (PLFAs) confirmed that heterotrophic bacteria may assimilate 13CO2 into cell macromolecules such as membrane lipids. All major PLFAs extracted from activated sludge and drinking water biofilm samples were enriched in 13C after incubation with CO2. Between 1.4% and 6.5% of the biomass produced by cultures of P. putida and a drinking water biofilm during growth in complex media was apparently derived from assimilation of CO2. Resting cells assimilated less CO2 compared to actively growing cells, and CO2 assimilation activity correlated with the amount of biomass produced during heterotrophic growth. The 14CO2 assimilation assay was evaluated as a tool to examine inhibitory effects of biocides on planktonic and sessile heterotrophs (biofilms). On the basis of 14CO2 assimilation activity, the minimum inhibitory concentration (MIC) of benzalkonium chloride was estimated to 21.1 and 127.2 mg l(-1) for planktonic and biofilm samples, respectively. The results indicate that assimilation of isotopically labelled CO2 can be used as a relatively simple measure of metabolic activity in heterotrophic bacteria. CO2 assimilation assays may be used to study the effects of antimicrobial agents on growth and survival of planktonic and sessile heterotrophic organisms.     

Evolution under pH stress and high population densities leads to increased density-dependent fitness in the protist Tetrahymena thermophila

Abiotic stress is a major force of selection that organisms are constantly facing. While the evolutionary effects of various stressors have been broadly studied, it is only more recently that the relevance of interactions between evolution and underlying ecological conditions, that is, eco-evolutionary feedbacks, have been highlighted. Here, we experimentally investigated how populations adapt to pH-stress under high population densities. Using the protist species Tetrahymena thermophila, we studied how four different genotypes evolved in response to stressfully low pH conditions and high population densities. We found that genotypes underwent evolutionary changes, some shifting up and others shifting down their intrinsic rates of increase (r₀). Overall, evolution at low pH led to the convergence of r₀ and intraspecific competitive ability (α) across the four genotypes. Given the strong correlation between r₀ and α, we argue that this convergence was a consequence of selection for increased density-dependent fitness at low pH under the experienced high density conditions. Increased density-dependent fitness was either attained through increase in r₀, or decrease of α, depending on the genetic background. In conclusion, we show that demography can influence the direction of evolution under abiotic stress.     

A small population of planktonic Flavobacteria with disproportionally high growth during the spring phytoplankton bloom in a prealpine lake

Bacterioplankton growth in temperate Lake Zurich (Switzerland) was studied during the spring phytoplankton bloom by in situ techniques and short-term dilution bioassays. A peak of chlorophyll a (Chl a ) concentrations was followed by a rise of bacterial cell numbers and leucine assimilation rates, of the proportions of cells incorporating 5-bromo-2-deoxyuridine (BrdU), and of community net growth rates in dilution cultures. Incorporation of BrdU was low in Betaproteobacteria (2 ± 1%), indicating that these bacteria did not incorporate the tracer. Pronounced growth of Betaproteobacteria in the enrichments was only observed after the decline of the phytoplankton bloom. An initial peak in the proportions of BrdU-positive Actinobacteria (30%) preceded a distinct rise of their cell numbers during the period of the Chl a maximum. Cytophaga–Flavobacteria (CF) changed little in numbers, but featured high proportions of BrdU-positive cells (28 ± 12%). Moreover, CF represented > 90% of all newly formed cells in dilution cultures before and during the phytoplankton bloom. One phylogenetic lineage of cultivable Flavobacteria (FLAV2) represented a small (0.5–1%) but highly active population in lake plankton. The growth rates of FLAV2 in dilution cultures doubled during the period of the Chl a maximum, indicating stimulation by phytoplankton exudates. Thus, CF, and specifically Flavobacteria , appeared to be substantially more important for carbon transfer in Lake Zurich spring bacterioplankton than was suggested by their standing stocks. The high in situ growth potential of these bacteria might have been counterbalanced by top-down control.     

Density-dependent dispersal and spatial distribution of a population

Many models have been proposed to suggest that animal dispersal enhances stability of an ecological system. However, little attention has been paid on the property of a boundary and on the size of a region. In this paper, we will consider the models proposed by Gurney & Nisbet (1975), from those points of view. We will show that, if a population is dispersing in a highly density-dependent manner, a stationary distribution which does not depend on boundary conditions is established in a finite region by interactions between the population and a heterogeneous environment. We will also show that, even when a population is confined in a habitat with a limited size a population dispersing density-dependently can establish a stationary distribution, whereas a population dispersing randomly either goes to extinction or grows explosively.     

On a population pathogen model incorporating species dispersal with temporal variation in dispersal rate

In the present paper, we consider a mathematical model of ecosystem population interaction where the population suffers from a susceptible–infectious–susceptible disease. Dispersal of both the susceptible and the infective is incorporated using reaction–diffusion equations. We first study the stability criteria of the basic (non-spatial) model around the disease-free and the infected steady states. We find that the loss rate of the infective species controls disease prevalence. Also without predation pressure, the disease will continue to exist among the population. Then we analyze the spatial model with species dispersal in constant as well as in time-varying form. It is observed that though constant dispersal is unable to generate diffusion-driven instability, dispersal with sinusoidal variation in dispersion rate can generate diffusive instability when the wave number of the perturbation lies within a given range. Numerical simulations are performed to illustrate analytical studies.     

Turnover and dispersal in a Peregrine Falco peregrinus population

In south Scotland, most Peregrines returned to the same territories to breed in successive years, though a few females changed territory from one year to the next.
Annual mortality among breeding birds was at most 9% among females (or 11% in both sexes combined). There may have been considerable annual variation, however, and excluding one exceptional year out of five reduced the estimate for females to 7%. These estimates are maxima, but are still considerably lower than those obtained from ring recoveries of dead birds reported by members of the public.
Among trapped birds, four males first bred at age two years, one at three and another at four or five; two females first bred at one year, 13 at two years old and one at three. Five other females which were seen to be in first-year plumage but were not trapped, also laid eggs, and 12 other such paired females held territory but did not lay. Only one paired male held territory in first-year plumage.
In their movements between natal and breeding territories, some females moved further than males, with median distances of 83 and 58 km respectively. In addition, of birds trapped breeding in the study area, a greater proportion of the males than of the females had been born locally, despite an equal sex ratio among fledglings; this was also consistent with a greater dispersal of females. In general, Peregrines made much longer movements in their first year of life than subsequently. Movements were in any direction.