Dark diversity in Amazonian stream fish communities: What factors determine species absence along environmental gradients?

1. Species distribution models often fail to predict observed patterns of species diversity, and this is because some species within a regional pool that are tolerant of conditions at a given location may nevertheless be absent from the local community. These missing species have been termed “dark diversity”. In the present study, we investigated which factors explain dark diversity among fish assemblages in Amazonian streams.
2. We sampled 71 streams in areas with different types of land use within two river basins and estimated dark diversity from patterns of species co-occurrence, using Beals’ index, along environmental gradients. From this procedure, taxa are designated as dark diversity components when they are absent from a given stream, but often co-occur with the local species at other streams, indicating similar ecological requirements. We used generalised linear models both to determine whether environmental or landscape variables, connectivity, instream environmental heterogeneity or some combination of these factors explained dark diversity of fishes, and to evaluate whether ecomorphology is associated with the extent to which a species contributes to dark diversity and which specific traits contribute the most to explaining variation in dark diversity.
3. Mean local diversity exceeded observed dark diversity. The magnitude of dark diversity was directly associated with the proportion of secondary forest in the immediate catchment and with the index of proximity to anthropogenic impact. Species that have high affinity for environments with higher current velocity, low swimming ability and that capture food mainly on the surface contributed more to dark diversity, which suggests that swimming ability, habitat preference and aspects related to diet are key predictors of the probability that a given species will be present at locations with suitable habitat.
4. Our findings reinforce the idea that dark diversity results from interactions between species traits and environmental factors, including anthropogenic impacts. Understanding the interplay among environmental factors and species traits that contribute to dark diversity provides targets for improved ecosystem restoration and sustainability of native species assemblages.

     

Testing for deterministic succession in metazoan parasite communities of marine fish

Parasite communities are similar to free‐living communities; decay of similarity over geographic distance, theory of island biogeography, species–area relationships and nestedness have been documented in both communities. Ecological succession has been studied in free‐living communities but has rarely been examined in parasite communities. We use seriation with replication to test the hypothesis that succession of parasite community structure is deterministic, thus developing throughout consecutive changes along the fish ontogeny, via a seriated pattern. 12 306 marine fishes (95 species) were studied. In 40 species, a seriated pattern was detected; 25 had a tendency towards a seriated pattern, and for 31 species, succession was at random. Age‐classes for each host species explained deterministic successional patterns for whole parasite communities and ectoparasites. Richness and number of age‐classes explained this pattern for endoparasites. Seriated successional pattern was evident for parasite communities of long‐lived marine fish, indicating that parasite communities follow sequential changes over time, like many free‐living communities.     

Beyond the green: assessing quarry restoration success through plant and beetle communities

In assessing the effectiveness of ecological restoration actions, outcomes evaluation using a multi‐taxa approach can greatly contribute to a clearer understanding of their success/failure. Since comprehensive biodiversity assessments are rarely possible, choosing taxa groups that are indicative of the ecosystem's structural and functional recovery is of major importance. Our goal was to evaluate the success of revegetation actions performed in a Mediterranean limestone quarry, using plants and epigean beetles as indicators. We compared their abundance, diversity, and community composition between revegetated sites aged 5, 13, and 19 years and a natural reference. Total plant cover significantly increased with restoration age and quickly reached reference values. However, native woody species cover dropped in the oldest site, while non‐native species became dominant. The abundance of beetles was always lower in restoration sites when compared to the reference, increasing with age, although not significantly. The richness of both plant species and beetle families was lower in restoration sites and did not show any trend towards the reference values. Finally, using nonmetric multidimensional scaling, the composition of plant and beetle communities from restoration sites showed a clear separation from the reference. Restoration efforts have successfully modified post‐quarry sites, but considerable differences remain, probably largely related to the use of the non‐native species Pinus halepensis in restoration plans. P. halepensis high cover in restoration sites greatly affects the structure of the ecosystem, and most likely its functioning too, as well as related ecosystem services, causing divergence from the reference values and compromising restoration success.     

Analysis of polysaccharide hydrolases secreted by Aspergillus flavipes FP-500 on corn cobs and wheat bran as complex carbon sources

Abstract

Aspergillus flavipes FP-500 is a Mexican native strain that has been reported as a good producer of xylanases and pectinases; therefore, it promises a strong impact on biotechnology. To provide an overview of protein secretion by A. flavipes, we carried out a comparative proteome analysis of extracellular proteins in liquid cultures with two heterogeneous agro-industrial residues; corn cob (CC) and wheat bran (WB), as carbon sources. Extracellular proteins obtained from both cultures were identified using MS/MS spectrometry. We identified 134 proteins, which were classified into four groups: glycosyl hydrolases (GH), esterases/proteases, miscellaneous proteins, and unidentified proteins. Around 50% of the total proteins identified were GH such as xylanases, β-xylosidases, β-galactosidases, cellulolytic enzymes like β-glucosidase, endoglucanases, and cellobiohydrolases. From this family, a core of 22 (16%) of the proteins identified were found in both substrates, CC and WB, whereas 30% and 54% were unique for CC and WB, respectively. In the esterases/proteases group, proteases, lipases and esterases like feruloylesterases, and acetyl-xylanesterase were identified. Proteins with diverse functions such as monophosphate dehydrogenase or N-acetylglucosaminidase were present. Here, we present strong evidences indicating that the composition and heterogeneity of the used carbon source determine the specific set of protein secreted by the fungus.     

Investigation of Ixodid ticks as vectors of Babesia caballi and Theileria equi (Protozoa: Apicomplexa) in central Italy

Babesia caballi and Theileria equi are widely recognized as causative agents of equine pirolasmosis (EP), an acute, sub‐acute, and chronic disease of equines, with relevant economic impact on horse trade worldwide. Although several studies on EP prevalence from central Italy have been published, data on ticks responsible for its transmission are still lacking. In this study, we identified a potential competent vector, investigating main features of its ecology together with EP infection rates. A two‐year sampling of questing ticks was carried out for the first time in Italy in an area known for high EP prevalence in horse sera, detecting the association between Rhipicephalus bursa and causative agents of EP. Most of the positive pools harbored a single infection (91.1%); mixed infections were also detected (8.9%). The infection rate for T. equi slightly decreased among years; B. caballi showed a lower, but increasing, infection rate. Tick phenology, climate variables, and peaks of EP prevalence indicated late May and second half of June as periods with the highest risk of new infections, especially during warm and dry days.     

The effect of riverine networks on fish β-diversity patterns in a Neotropical system

Hydrobiologia - We investigated how the riverine network influences taxonomic and functional beta diversity patterns of fish assemblages in the mainstem/headwater (lateral) and upstream/downstream...     

The effects of food quantity,light, and temperature on clearance rates in freshwater bivalves (Cyrenidae and Unionidae)

Hydrobiologia - Assessing the environmental variables that influence freshwater bivalve filtration activity is key to better understand the functioning of stream ecosystems. In the present study,...