Habitat Complexity Enhances Comminution and Decomposition Processes in Urban Ecosystems

Decomposition of organic matter is an essential process regulating fluxes of energy and matter within ecosystems. Although soil microbes drive decomposition, this is often facilitated by detritivores through comminution. The contribution of detritivores and microbes to comminution and decomposition processes is likely to be affected by the habitat complexity. In urban ecosystems, human activities and management of vegetation and litter and soil components determine habitat complexities unobserved in natural ecosystems. Therefore, we investigated the effect of habitat complexity of low- and high-complexity urban parks and high-complexity woodland remnants on microbial decomposition and detritivore comminution using litter bags of differing mesh size. Detritivores were sampled using pitfall traps and their assemblage structure related to rates of comminution. Habitats of lower complexity had significantly lower decomposition and comminution rates. In more complex habitats, site history did not affect decomposition and comminution processes. Vegetation complexity and the indirect effect on microclimate explained most of the variation in decomposition and comminution processes. The abundance of macrofauna detritivores and their species richness were both positively related to higher comminution rates. The volume of understory vegetation was the best predictor for both macrofauna detritivore assemblage structure and comminution and decomposition processes. The study demonstrated that relatively modest changes in habitat complexity associated with different management practices can exert significant effects on the decomposition and comminution processes. The structure of detritivores assemblages was also subjected to modifications of the habitat complexity with significant effects on comminution processes. Simple management practices aimed to increase the complexity of habitats, particularly in the understory vegetation and litter layers, could restore and enhance soil biodiversity and functioning in urban ecosystems.     

Hydrologic Variability Affects Invertebrate Grazing on Phototrophic Biofilms in Stream Microcosms

The temporal variability of streamflow is known to be a key feature structuring and controlling fluvial ecological communities and ecosystem processes. Although alterations of streamflow regime due to habitat fragmentation or other anthropogenic factors are ubiquitous, a quantitative understanding of their implications on ecosystem structure and function is far from complete. Here, by experimenting with two contrasting flow regimes in stream microcosms, we provide a novel mechanistic explanation for how fluctuating flow regimes may affect grazing of phototrophic biofilms (i.e., periphyton) by an invertebrate species (Ecdyonurus sp.). In both flow regimes light availability was manipulated as a control on autotroph biofilm productivity and grazer activity, thereby allowing the test of flow regime effects across various ratios of biofilm biomass to grazing activity. Average grazing rates were significantly enhanced under variable flow conditions and this effect was highest at intermediate light availability. Our results suggest that stochastic flow regimes, characterised by suitable fluctuations and temporal persistence, may offer increased windows of opportunity for grazing under favourable shear stress conditions. This bears important implications for the development of comprehensive schemes for water resources management and for the understanding of trophic carbon transfer in stream food webs.     

Coexistence of Genetically Engineered Escherichia coliStrains and Natural Microorganisms in Experimental Aquatic Microcosms

In experimental aquatic microcosms (AMCs), the population of the Escherichia colistrain Z905 harboring the recombinant plasmid pPHL7 (Ap^rLux⁺) was found to gradually accumulate AMC-adapted cells, which retained the plasmid but differed from the original cells in some biochemical and physiological characteristics. Both the original and the AMC-adaptedE. colicells could coexist with the native AMC microflora for one year or longer. When introduced into AMCs together with native pseudomonads, the AMC-adapted E. coliZ905-33 (pPHL7) cells were more competitive than the nonadapted cells.     

Complexity and Specificity of Precursor microRNAs Driven by Transposable Elements in Rice

In eukaryotes, small noncoding RNA molecules of 16–29 nucleotides in length play crucial roles in the regulation of gene expression. Some 377 sequences representing rice pseudo-microRNAs (miRNAs) are available in release 13.0 of the miRBase sequence database () and are grouped into 143 families. Most newly deposited miRNA sequences are likely to be species-specific. To understand the relationship between miRNAs and transposable elements (TEs) in rice, the RepeatMasker application () was used to screen single-stranded precursor miRNA (pre-miRNA) sequences. This analysis revealed that 33.1% of miRNAs and 36.4% of miRNA families are associated with interspersed repeats, and most of them are species-specific. Furthermore, multiple miRNA families can be encoded by the same TE class. Alignment analysis revealed that miR439 originated from an MuDR4-OS TE, which amplified and diversified in the genome as an inverted repeat of the core sequence followed by multiple repeats. Multiple copies of miR445 and its complexity originate from and are driven by the DNA/Tourist TE class. These results provide an important contribution to the elucidation of TE-driven mechanisms that regulate the species specificity and complexity of rice miRNAs.     

The Role of Habitat Complexity in Community Development Is Mediated by Resource Availability

Habitat complexity strongly affects the structure and dynamics of ecological communities, with increased complexity often leading to greater species diversity and abundance. However, habitat complexity changes as communities develop, and some species alter their environment to themselves provide habitat for other species. Most experimental studies manipulate basal substrate complexity, and while the importance of complexity likely changes during community development, few studies have examined the temporal dynamics of this variable. We used two experiments to quantify the importance of basal substrate complexity to sessile marine invertebrate community development through space and time. First, we compared effects of substrate complexity at 70 sites across ten estuaries. Sites differed in recruitment and community development rates, and after three months provided spatial variation in community development stage. Second, we tested for effects of substrate complexity at multiple times at a single site. In both experiments, complexity affected marine sessile invertebrate community composition in the early stages of community development when resource availability was high. Effects of complexity diminished through time as the amount of available space (the primary limiting resource) declined. Our work suggests the presence of a bare-space threshold, at which structural complexity of the basal substrate is overwhelmed by secondary biotic complexity. This threshold will be met at different times depending on local recruitment and growth rates and is likely to vary with productivity gradients.     

Learning to Avoid Dangerous Habitat Types by Aquatic Salamanders,Eurycea tynerensis

There should be intense selection for predation avoidance mechanisms when prey live in close proximity to their predators. Prey individuals that can learn to associate habitat features with high levels of predation risk should experience increased survival if they subsequently avoid those habitats. We tested whether or not habitat learning occurred in a benthic stream community consisting of adult Oklahoma salamander (Eurycea tynerensis) prey and a syntopic predatory fish, the banded sculpin (Cottus carolinae). We exposed individual salamanders to chemical stimuli from sculpin, non‐predatory tadpoles, or a blank control in training tanks containing either rocks or grass. Two days later, the salamanders were tested in tanks that offered a choice of rocks or grass. Salamanders showed significant avoidance of the habitat where they had previously encountered chemical cues from sculpin in comparison to the non‐predatory controls. Learning to avoid dangerous habitats may be particularly important for prey whose predators are visually cryptic ambush foragers, such as sculpin.     

Survival and Impact of Genetically Engineered Pseudomonas putida Harboring Mercury Resistance Gene in Aquatic Microcosms

The survival of wild-type and genetically engineered Pseudomonas putida PpY101 that contained a recombinant plasmid pSR134 conferring mercury resistance were monitored in aquatic microcosms. We used lake, river, and spring water samples. The density of genetically engineered and wild-type P. putida decreased rapidly within 5 days (population change rate k -0.87 ~ -1.00 day^?1), then moderately after 5 to 28 days (-0.10~, -0.14 day^?1). The population change rates of genetically engineered and wild-type P. putida were not significantly different. We studied the important factors affecting the survival of genetically engineered and wild-type P. putida introduced in aquatic microcosms. Visible light exerted an adverse effect on the survival of the two strains. The densities of genetically engineered and wild-type P. putida were almost constant until 7 days after inoculation in natural water filtered with a 0.45-µm membrane filter, or treated with cycloheximide to inhibit the growth of protozoa. These results suggested that protozoan predation was one of the most important factors for the survival of two strains. We examined the impact of the addition of genetically engineered and wild-type P. putida on indigenous bacteria and protozoa. Inoculation of genetically engineered or wild-type P. putida had no apparent effect on the density of indigenous bacteria. The density of protozoa increased in microcosms inoculated with genetically engineered or wild-type P. putida at 3 days after inoculation, but after 5 to 21 days, the density of protozoa decreased to the same level as the control microcosms.     

Carcass Type Affects Local Scavenger Guilds More than Habitat Connectivity

Scavengers and decomposers provide an important ecosystem service by removing carrion from the environment. Scavenging and decomposition are known to be temperature-dependent, but less is known about other factors that might affect carrion removal. We conducted an experiment in which we manipulated combinations of patch connectivity and carcass type, and measured responses by local scavenger guilds along with aspects of carcass depletion. We conducted twelve, 1-month trials in which five raccoon (Procyon lotor), Virginia opossum (Didelphis virginiana), and domestic rabbit (Oryctolagus spp.) carcasses (180 trials total) were monitored using remote cameras in 21 forest patches in north-central Indiana, USA. Of 143 trials with complete data, we identified fifteen species of vertebrate scavengers divided evenly among mammalian (N = 8) and avian species (N = 7). Fourteen carcasses (9.8%) were completely consumed by invertebrates, vertebrates exhibited scavenging behavior at 125 carcasses (87.4%), and four carcasses (2.8%) remained unexploited. Among vertebrates, mammals scavenged 106 carcasses, birds scavenged 88 carcasses, and mammals and birds scavenged 69 carcasses. Contrary to our expectations, carcass type affected the assemblage of local scavenger guilds more than patch connectivity. However, neither carcass type nor connectivity explained variation in temporal measures of carcass removal. Interestingly, increasing richness of local vertebrate scavenger guilds contributed moderately to rates of carrion removal (≈6% per species increase in richness). We conclude that scavenger-specific differences in carrion utilization exist among carcass types and that reliable delivery of carrion removal as an ecosystem service may depend on robust vertebrate and invertebrate communities acting synergistically.     

Performance Trade-offs Driven by Morphological Plasticity Contribute to Habitat Specialization of Bornean Tree Species

Growth-survival trade-offs play an important role in niche differentiation of tropical tree species in relation to light-gradient partitioning. However, the mechanisms that determine differential species performance in response to light and soil resource availability are poorly understood. To examine responses to light and soil nutrient availability, we grew seedlings of five tropical tree species for 12 mo at < 2 and 18 percent full sunlight and in two soil types representing natural contrasts in nutrient availability within a lowland dipterocarp forest in North Borneo. We chose two specialists of nutrient-rich and nutrient-poor soils, respectively, and one habitat generalist. Across all species, growth was higher in high than low light and on more nutrient rich soil. Although species differed in growth rates, the ranking of species, in terms of growth, was consistent across the four treatments. Nutrient-rich soils improved seedling survival and increased growth of three species even under low light. Slower-growing species increased root allocation and reduced specific leaf area (SLA) and leaf area ratio (LAR) in response to decreased nutrient supply. All species increased LAR in response to low light. Maximum growth rates were negatively correlated with survival in the most resource-limited environment. Nutrient-poor soil specialists had low maximum growth rates but high survival at low resource availability. Specialists of nutrient-rich soils, plus the habitat generalist, had the opposite suite of traits. Fitness component trade-offs may be driven by both light and belowground resource availability. These trade-offs contribute to differentiation of tropical tree species among habitats defined by edaphic variation.     

Genetically Engineered Erwinia carotovora in Aquatic Microcosms: Survival and Effects on Functional Groups of Indigenous Bacteria

The survival of genetically engineered Erwinia carotovora L-864, with a kanamycin resistance gene inserted in its chromosome, was monitored in the water and sediment of aquatic microcosms. The density of genetically engineered and wild-type E. carotovora strains declined at the same rate, falling in 32 days below the level of detection by viable counts. We examined the impact of the addition of genetically engineered and wild-type strains on indigenous bacteria belonging to specific functional groups important in nutrient cycling. For up to 16 days, the densities of total and proteolytic bacteria were significantly higher (P < 0.05) in microcosms inoculated with genetically engineered or wild-type E. carotovora, but by 32 days after inoculation, they had decreased to densities similar to those in control microcosms. Inoculation of genetically engineered or wild-type E. carotovora had no apparent effect on the density of amylolytic and pectolytic bacteria in water and sediment. Genetically engineered and wild-type E. carotovora did not have significantly different effects on the densities of specific functional groups of indigenous bacteria (P > 0.05).     

Predation Threat Affects Behaviour and Habitat Use by Hatchery Brown Trout (Salmo Trutta L.) Juveniles

The effect of predation threat on behaviour and habitat use by brown trout (Salmo trutta L.) juveniles were studied in four indoor and six outdoor experimental channels. Northern pike (Esox lucius L.) was used as a predator. Brown trout were more active during the night compared to day, but in the presence of pike the increase in activity was less than in treatments without predator. Aggressive interactions between trout were higher during the day when pike was absent. In the presence of pike trout tended to use more coarse substrate classes as subdominant habitat suggesting increased use of cover and also higher or lower water depths. Our results increase knowledge of the effects of predation threat on habitat selection and behaviour by brown trout.     

Developmental status of Aquatic Animal Experiment Facility, Aquatic Habitat (AQH), for International Space Station.

Mitsubishi Heavy Industries (MHI) and Japan Aerospace Exploration Agency (JAXA) have been studying Aquatic Animal Experiment Facility, Aquatic Habitat (AQH), for International Space Station (ISS). The AQH will have the capabilities to accommodate small freshwater fish and amphibian for maximum 90 days on orbit. Three-generations of small freshwater fish (medaka and zebrafish), and egg through metamorphosis of amphibian (African clawed toad) could be experimented by AQH. Various experimental functions such as automatic feeding, air-water interface, day/night cycle, video observation, and specimen sampling mechanism will be also equipped in AQH. The water circulation system was improved from the past aquatic facilities for Space Shuttle experiments under the consideration of the long life-time, and a brand-new specimen chamber was developed to equip the above various experimental functions. Currently the prototype model of water circulation system and specimen chambers have been manufactured and biological compatibility tests are being conducted with medaka. The current developmental status of AQH is summarized.     

Estimating Fish Exploitation and Aquatic Habitat Loss across Diffuse Inland Recreational Fisheries

The current state of many freshwater fish stocks worldwide is largely unknown but suspected to be vulnerable to exploitation from recreational fisheries and habitat degradation. Both these factors, combined with complex ecological dynamics and the diffuse nature of inland fisheries could lead to an invisible collapse: the drastic decline in fish stocks without great public or management awareness. In this study we provide a method to address the pervasive knowledge gaps in regional rates of exploitation and habitat degradation, and demonstrate its use in one of North America’s largest and most diffuse recreational freshwater fisheries (Ontario, Canada). We estimated that 1) fish stocks were highly exploited and in apparent danger of collapse in management zones close to large population centres, and 2) fish habitat was under a low but constant threat of degradation at rates comparable to deforestation in Ontario and throughout Canada. These findings confirm some commonly held, but difficult to quantify, beliefs in inland fisheries management but also provide some further insights including 1) large anthropogenic projects greater than one hectare could contribute much more to fish habitat loss on an area basis than the cumulative effect of smaller projects within one year, 2) hooking mortality from catch-and-release fisheries is likely a greater source of mortality than the harvest itself, and 3) in most northern management zones over 50% of the fisheries resources are not yet accessible to anglers. While this model primarily provides a framework to prioritize management decisions and further targeted stock assessments, we note that our regional estimates of fisheries productivity and exploitation were similar to broadscale monitoring efforts by the Province of Ontario. We discuss the policy implications from our results and extending the model to other jurisdictions and countries.     

Seasonal Habitat Use of Agoutis (Dasyprocta azarae) is Driven by the Palm Attalea phalerata in Brazilian Pantanal

Resource availability can influence animal movement causing changes in home‐range size and arrangement between seasons. We investigated the influence of acuri palm (Attalea phalerata) on the occupancy of agouti Dasyprocta azare during both the dry and rainy seasons, as well as the abandonment probabilities in the transition between seasons in the Brazilian Pantanal. The agoutis occupied a high proportion of the forested areas in the rainy season (0.83), but the occupancy decreased in the dry season (0.39). In the rainy season, occupancy by agoutis was not correlated with acuri palm availability, while in the dry season, it was positively correlated with the palm's availability. The acuri palm availability also drove the agoutis' probability of site abandonment from the rainy to the dry season, with higher abandonment probability in sites with low acuri palm availability. These findings show that this large‐seeded palm can be an important resource for the agoutis' populations during the fruit‐scarcity period. The acuri palm seeds may be particularly important for agoutis using fragmented forests, given that the large‐seeded palms are able to persist even in small fragments, which is untrue for other important resource.     

Indigenous Microbiota and Habitat Influence Escherichia coli Survival More than Sunlight in Simulated Aquatic Environments

The reported fate of Escherichia coli in the environment ranges from extended persistence to rapid decline. Incomplete understanding of factors that influence survival hinders risk assessment and modeling of the fate of fecal indicator bacteria (FIB) and pathogens. FIB persistence in subtropical aquatic environments was explored in outdoor mesocosms inoculated with five E. coli strains. The manipulated environmental factors were (i) presence or absence of indigenous microbiota (attained by natural, disinfected, and cycloheximide treatments), (ii) freshwater versus seawater, and (iii) water column versus sediment matrices. When indigenous microbes were removed (disinfected), E. coli concentrations decreased little despite exposure to sunlight. Conversely, under conditions that included the indigenous microbiota (natural), significantly greater declines in E. coli occurred regardless of the habitat. The presence of indigenous microbiota and matrix significantly influenced E. coli decline, but their relative importance differed in freshwater versus seawater. Cycloheximide, which inhibits protein synthesis in eukaryotes, significantly diminished the magnitude of E. coli decline in water but not in sediments. The inactivation of protozoa and bacterial competitors (disinfected) caused a greater decline in E. coli than cycloheximide alone in water and sediments. These results indicate that the autochthonous microbiota are an important contributor to the decline of E. coli in fresh and seawater subtropical systems, but their relative contribution is habitat dependent. This work advances our understanding of how interactions with autochthonous microbiota influence the fate of E. coli in aquatic environments and provides the framework for studies of the ecology of enteric pathogens and other allochthonous bacteria in similar environments.     

Development of Vegetation and Aquatic Habitat in Restored Riparian Sites of California's North Coast Rangelands

The preponderance of short‐term objectives and lack of systematic monitoring of restoration projects limits opportunities to learn from past experience and improve future restoration efforts. We conducted a retrospective, cross‐sectional survey of 89 riparian revegetation sites and 13 nonrestored sites. We evaluated 36 restoration metrics at each site and used project age (0–39 years) to quantify plant community and aquatic habitat trajectories with a maximum likelihood model selection approach to compare linear and polynomial relationships. We found significant correlations with project age for 16 of 21 riparian vegetation, and 11 of 15 aquatic habitat attributes. Our results indicated improvements in multiple ecosystem services and watershed functions such as diversity, sedimentation, carbon sequestration, and available habitat. Ten riparian vegetation metrics, including native tree and exotic shrub density, increased nonlinearly with project age, while litter and native shrub density increased linearly. Species richness and cover of annual plants declined over time. Improvements in aquatic habitat metrics, such as increasing pool depth and decreasing bankfull width‐to‐depth ratio, indicated potentially improved anadromous fish habitats at restored sites. We hypothesize that certain instream metrics did not improve because of spatial and/or temporal limitations of riparian vegetation to affect aquatic habitat. Restoration managers should be prepared to maintain or enhance understory diversity by controlling exotic shrubs or planting shade‐tolerant native species as much as 10 years after revegetation.     

The Influence of Habitat Complexity on Reef Fish Communities in the Northeastern Gulf of Mexico

Several previous studies have attempted to correlate habitat complexity and reef fish species diversity. These studies have mostly examined natural reef systems, but results differed. To examine this relation, we built 1 m² habitats with 20 replicates of five complexity levels from July to August 2001 in the northeastern Gulf of Mexico (n=100). In June and July 2002, we built new habitats using the 2001 design, but also added a sixth complexity level (n=120). In order of increasing complexity these included: cage, shell, cage-shell, block-shell, cage-block-shell, and shell-block-pyramid habitats. Most fish in both years were juveniles and included species common to reef structures in the northeastern Gulf of Mexico. In 2001, we identified 26 fish species, and the dominant species was red snapper, Lutjanus campechanus (41%), followed by rock sea bass, Centropristis philadelphica (23%), and sand perch, Diplectrum spp. (14%). In 2002 we identified 36 species, and the dominant species was tomtate, Haemulon aurolineatum (36%), followed by Diplectrum spp. (19%), and L. campechanus (13%). In 2001, species diversity and richness were significantly (P<0.05) higher on more complex habitats (H′=1.7, S=11–12) compared to less complex habitats (H′=0.8–1.0, S=4–9). In 2002, patterns among diversity, richness and reef complexity were less apparent with only the least complex habitats shell and cage showing significantly lower values. In both years, multidimensional scaling grouped by complexity levels with cage and shell habitats showing the clearest separation from other habitat types. Also, with few exceptions (only 8%) analysis of similarities showed significant (P<0.05) differences in fish communities across complexity levels. Although community composition varied between years, this study provided evidence to support the hypothesis that habitat complexity increased reef fish species diversity.     

Ectopic Expression of Erigeron breviscapus JAZ1 Affects JA-Induced Development Processes in Transgenic Arabidopsis

The jasmonate ZIM-domain (JAZ) proteins are repressors that function in the regulation of plant growth, development, and response to stimulation of different signals in the JA signaling pathway. Erigeron breviscapus is characteristic of sporophyte self-incompatibility (SSI). However, whether JA signaling is involved in regulation of development processes in E. breviscapus is unclear. In this study, the JAZ homolog EbJAZ1 was isolated and characterized from E. breviscapus. EbJAZ1 was localized to the nucleus, and expressed in roots, stems, leaves and flowers. Ectopic expression of EbJAZ1 in Arabidopsis resulted in shorter filament and silique length, and lower seed fertility. In addition, MeJA-induced root growth inhibition was compromised in transgenic plants. Further qRT-PCR analysis indicated that expression patterns of marker genes for VSP1, VSP2, JAZ1, JAZ5, JAZ8, JAZ10, MYC2, and bHLH17 were downregulated in transgenic plants compared to wild-type, suggesting that EbJAZ regulates the development of flower organs, seed fertility, and primary root growth through the JA signaling pathway. Thus, our results indicate that EbJAZ1 is one of the important regulators possibly involved in SSI and other developmental processes in Erigeron breviscapus.

     

Task Complexity Differentially Affects Executed and Imagined Movement Preparation: Evidence from Movement-Related Potentials

Background

The neural simulation theory predicts similarity for the neural mechanisms subserving overt (motor execution) and covert (movement imagination) actions. Here we tested this prediction for movement preparation, a key characteristic of motor cognition.

Methodology/Principal Findings

High-density electroencephalogram (EEG) was recorded during covert and overt actions. Movement preparation was studied with a motor priming paradigm, which varied task complexity and amount of advance information. Participants performed simple or complex sequential finger movements either overtly or covertly. Advance information was either fully predictive or partially predictive. Stimulus-locked event-related potential (ERP) data showed the typical pattern of foreperiod activation for overt and covert movements. The foreperiod contingent negative variation (CNV) differed between simple and complex movements only in the execution task. ERP topographies differed between execution and imagination only when advance information was fully predictive.

Conclusions/Significance

Results suggest a differential contribution of the movement preparation network to action imagination and execution. Overt and covert actions seem to involve similar though not identical mechanisms, where overt actions engage a more fine-grained modulation of covert preparatory states.