Microbial population dynamics in the faeces of wood‐eating loricariid catfishes

Catfishes of the genus Panaque are known for their ability to feed on wood and hence to process cellulose fibres in their digestive systems. The paper industry uses cellulose fibres and thus has an interest in exploiting this property biomimetically: it could be employed as a pretreatment to lessen the energy required by the mechanical production stage of manufacturing nanocellulose fibres. Here, we characterize the diet‐associated in situ microbial diversity and population dynamic in the faeces of catfish (Panaque sp.) exposed to consecutive diets of pellet food and then wood. Fish faeces samples were collected and investigated by parallel DNA deep amplicon sequencing of the bacterial 16S rRNA SSU for both diet conditions. The most frequently occurring bacterium in the faeces was Cetobacterium sp. The dominant cellulolytic bacterial genera found in ascending relative abundance were as follows: Aeromonas sp., Flavobacterium sp., Bacteroides sp., Pseudomonas sp. and Cellvibrio sp. Diet‐associated changes in the faeces microbiome were noted for Flavobacterium sp. Extensive microbial diversity was found in catfish faeces, evidenced using culture‐independent molecular techniques. No significant diet‐associated effects on the microbiome in terms of biodiversity were observed in the catfish faeces, but diet‐associated changes in the microbial population structure were observed.

Significance and Impact of the Study

Although catfishes are not classified as true xylivores, inhabiting their faeces are bacteria that may provide a novel source of cellulolytic enzyme. Based on this first microbiology study, the faeces and thus the gastrointestinal microbiome of Panaque catfishes are an unexplored reservoir of microbial extracts with enhanced polysaccharide transforming enzyme activity. The biomimetical exploitation of this cellulolytic activity in the form of novel enzymes or by applying a mixture of cellulolytic micro‐organisms could accomplish a pretreatment to the mechanical production process of nanocellulose fibres, thus could reduce the energy consumption costs significantly.     

Mechanisms of chromosomal evolution and its possible relation to natural history characteristics in Ancistrus catfishes (Siluriformes: Loricariidae)

Ancistrus is the most speciose genus of the tribe Ancistrini, with 58 valid species and many yet to be described. Cytogenetic studies were conducted on five apparently undescribed species from the Amazon basin, which showed different diploid numbers: Ancistrus sp. Purus (2n = 34); Ancistrus sp. Macoari (2n = 46); Ancistrus sp. Dimona (2n = 52); Ancistrus sp. Vermelho (2n = 42) and Ancistrus sp. Trombetas (2n = 38). All species possessed only one pair of NOR‐carrying chromosomes, but with extensive variation in both the location on the chromosome as well as in the position of the ribosomal sites on the karyotype. The karyotypic evolution of Ancistrus species seems to be based on chromosomal rearrangements, with a tendency to a reduction of the diploid number. Two new instances of XX/XY sex chromosomes for Ancistrus species, based on the heteromorphism in the male karyotype, were also recorded. The large karyotypic diversity among Ancistrus species may be related to biological and behavioural characteristics of these fish that include microhabitat preferences, territoriality and specialized reproductive tactics. These characteristics may lead to a fast rate of fixation of chromosomal mutations and eventually speciation across the basin.     

A new species of Sturisoma (Loricariidae: Loricariinae) from the Madre de Dios River basin,Peru, with a key to all congeners and comments on the type series of Sturisoma rostratum

A new species of the genus Sturisoma from the Madre de Dios River, upper Madeira, Peru, is described. The new species can be differentiated from its congeners by the following characteristics: dorsolateral stripe reaching to less than half, or only half length of caudal peduncle (v. absence of dorsolateral stripe or, if present, spanning more than half caudal‐peduncle length); premaxillary teeth longer than dentary teeth (v. dentary teeth longer); sexually mature adult males having well‐developed odontodes on the sides of the head and a broader snout (v. adult males lacking well‐developed hypertrophied odontodes or, if present, rostrum is same width as females' or immature males'); by having the ventral portion of the rostrum conspicuously darker than ventral surface of the body (v. rostrum light, with same colour as ventral portion of body, except in Sturisoma barbatum); by lacking the lateral process of the sphenotic (v. lateral process of sphenotic well‐developed, except in Sturisoma tenuirostre); a dark spot on the first three branched pectoral‐fin rays (v. brown spot absent, except in S. barbatum); and the frontal bone contributing less than half of dorsal border of the orbital ridge (v. extensive participation of the frontal, except in Sturisoma guentheri). Furthermore, the new species has 18–20 plates in the median series, which differentiates it from Sturisoma rostratum (21–22), and Sturisoma monopelte (21); and 14–15 coalescent plates, which differentiates it from S. tenuirostre (16–17). It is further differentiated from Sturisoma brevirostre by presence of an enlarged rostrum (v. rostrum not enlarged). A discussion regarding status of the type series and geographic distribution of Sturisoma rostratum is offered, and an identification key for all Sturisoma species is presented.     

Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology

The metabolic activities of gut microbes significantly influence host physiology; thus, characterizing the forces that modulate this micro‐ecosystem is key to understanding mammalian biology and fitness. To investigate the gut microbiome of wild primates and determine how these microbial communities respond to the host's external environment, we characterized faecal bacterial communities and, for the first time, gut metabolomes of four wild lowland gorilla groups in the Dzanga‐Sangha Protected Areas, Central African Republic. Results show that geographical range may be an important modulator of the gut microbiomes and metabolomes of these gorilla groups. Distinctions seemed to relate to feeding behaviour, implying energy harvest through increased fruit consumption or fermentation of highly fibrous foods. These observations were supported by differential abundance of metabolites and bacterial taxa associated with the metabolism of cellulose, phenolics, organic acids, simple sugars, lipids and sterols between gorillas occupying different geographical ranges. Additionally, the gut microbiomes of a gorilla group under increased anthropogenic pressure could always be distinguished from that of all other groups. By characterizing the interplay between environment, behaviour, diet and symbiotic gut microbes, we present an alternative perspective on primate ecology and on the forces that shape the gut microbiomes of wild primates from an evolutionary context.     

Gut microbiomes of free‐ranging and captive Namibian cheetahs: Diversity,putative functions and occurrence of potential pathogens

Although the significance of the gut microbiome for host health is well acknowledged, the impact of host traits and environmental factors on the interindividual variation of gut microbiomes of wildlife species is not well understood. Such information is essential; however, as changes in the composition of these microbial communities beyond the natural range might cause dysbiosis leading to increased susceptibility to infections. We examined the potential influence of sex, age, genetic relatedness, spatial tactics and the environment on the natural range of the gut microbiome diversity in free‐ranging Namibian cheetahs (Acinonyx jubatus). We further explored the impact of an altered diet and frequent contact with roaming dogs and cats on the occurrence of potential bacterial pathogens by comparing free‐ranging and captive individuals living under the same climatic conditions. Abundance patterns of particular bacterial genera differed between the sexes, and bacterial diversity and richness were higher in older (>3.5 years) than in younger individuals. In contrast, male spatial tactics, which probably influence host exposure to environmental bacteria, had no discernible effect on the gut microbiome. The profound resemblance of the gut microbiome of kin in contrast to nonkin suggests a predominant role of genetics in shaping bacterial community characteristics and functional similarities. We also detected various Operational Taxonomic Units (OTUs) assigned to potential pathogenic bacteria known to cause diseases in humans and wildlife species, such as Helicobacter spp., and Clostridium perfringens. Captive individuals did not differ in their microbial alpha diversity but exhibited higher abundances of OTUs related to potential pathogenic bacteria and shifts in disease‐associated functional pathways. Our study emphasizes the need to integrate ecological, genetic and pathogenic aspects to improve our comprehension of the main drivers of natural variation and shifts in gut microbial communities possibly affecting host health. This knowledge is essential for in situ and ex situ conservation management.     

The role of novel forest ecosystems in the conservation of wood‐inhabiting fungi in boreal broadleaved forests

The increasing human impact on the earth's biosphere is inflicting changes at all spatial scales. As well as deterioration and fragmentation of natural biological systems, these changes also led to other, unprecedented effects and emergence of novel habitats. In boreal zone, intensive forest management has negatively impacted a multitude of deadwood‐associated species. This is especially alarming given the important role wood‐inhabiting fungi have in the natural decay processes. In the boreal zone, natural broad‐leaved‐dominated, herb‐rich forests are threatened habitats which have high wood‐inhabiting fungal species richness. Fungal diversity in other broadleaved forest habitat types is poorly known. Traditional wood pastures and man‐made afforested fields are novel habitats that could potentially be important for wood‐inhabiting fungi. This study compares species richness and fungal community composition across the aforementioned habitat types, based on data collected for wood‐inhabiting fungi occupying all deadwood diameter fractions. Corticioid and polyporoid fungi were surveyed from 67 130 deadwood particles in four natural herb‐rich forests, four birch‐dominated wood pastures, and four birch‐dominated afforested field sites in central Finland. As predicted, natural herb‐rich forests were the most species‐rich habitat. However, afforested fields also had considerably higher overall species richness than wood pastures. Many rare or rarely collected species were detected in each forest type. Finally, fungal community composition showed some divergence not only among the different habitat types, but also among deadwood diameter fractions. Synthesis and applications: In order to maintain biodiversity at both local and regional scales, conserving threatened natural habitat types and managing traditional landscapes is essential. Man‐made secondary woody habitats could provide the necessary resources and serve as surrogate habitats for many broadleaved deadwood‐associated species, and thus complement the existing conservation network of natural forests.     

Community structure of polypores (Basidiomycota) in Andean alder wood in Argentina: Functional groups among wood‐decay fungi?

Abstract The polypores (Aphyllophorales s.l., Basidiomycota) are very effective wood decayers. Different species differ in their capacity to decay wood; therefore, many functionally different species can be found decaying different substrate conditions (decay stages and log diameter). This study aimed to describe the structure of the wood‐decay polypore communities that occur on different states of wood of the Andean alder (Alnus acuminata) within Argentina and to identify groups of polypore species that share the same substrate condition, and thus might have a similar functional role in the decay processes. We found 16 polypore species, among which Trametes versicolor, Bjerkandera adusta and Trametes cubensis were dominant species, showing the highest relative frequency in alder wood. Species richness was lower on trunks of living trees and higher on dead branches. Based on preferential occurrence on different wood conditions, a cluster analysis distinguished three groups, each of them containing one of the three dominant species. This corresponds to the situation of other groups of organisms, where each functional type consists of a dominant species that accounts for most of the ‘function’ and several subordinate species with similar functions. Albeit preliminary, our results provide a formal classification of wood‐decay fungi into functional types.     

Isolation and characterization of microsatellite loci in Pseudoplatystoma corruscans (Siluriformes: Pimelodidae) and cross‐species amplification

A total of five polymorphic microsatellites loci from Pseudoplatystoma corruscans were isolated and characterized. A population survey involving 43 specimens resolved a large number of alleles (range seven to eight among loci) and high observed heterozygosity (0.500–0.615), indicating its usefulness in population genetics studies. Cross‐species amplification was successful in four other Pimelodidae species.     

Occurrence patterns of aspen‐feeding wood‐borers (Coleoptera: Cerambycidae) along the wood decay gradient: active selection for specific host types or neutral mechanisms?

Abstract.  1. Determinants of host-use patterns in plant-feeding insects have been extensively studied, usually within the framework of optimality theory. Comparatively, factors driving host selection in saprophagous insects have received little attention.
2. In this study, mechanisms creating occurrence peaks of saprophagous wood-borers (Cerambycidae: Coleoptera) in standing dead aspen in the middle and late stages of decay were investigated by correlating insect occurrence with variations in substrate-related nutritional and physical parameters. Twenty-four snags at four decay stages were dissected from a mature stand in western Quebec, Canada. Wood samples were taken to measure levels of nitrogen, non-structural carbohydrates, phenols, wood density, water content and snag age.
3. Several nutritional and physical parameters varied significantly along the decay gradient and were correlated with insect occurrence, but all significant parameters were also strongly correlated with snag age and wood density. Model selection using Akaike's second order information criteria was used to rank the different models; the model including snag age only performed best, with a w_i of 0.873.
4. This importance of snag age gives support to a proposed hypothesis of host selection in which temporal autocorrelation in probability of insect occurrence explains peaks observed in the middle and late stages of decay. However, further studies will be needed to confirm the prevalence of such neutral mechanisms over active selection in the determination of host-use patterns in decaying aspen.     

A 7000‐year history of changing plant trait composition in an Amazonian landscape; the role of humans and climate

Tropical forests are shifting in species and trait composition, but the main underlying causes remain unclear because of the short temporal scales of most studies. Here, we develop a novel approach by linking functional trait data with 7000 years of forest dynamics from a fossil pollen record of Lake Sauce in the Peruvian Amazon. We evaluate how climate and human disturbances affect community trait composition. We found weak relationships between environmental conditions and traits at the taxon level, but strong effects for community‐mean traits. Overall, community‐mean traits were more responsive to human disturbances than to climate change; human‐induced erosion increased the dominance of dense‐wooded, non‐zoochorous species with compound leaves, and human‐induced fire increased the dominance of tall, zoochorous taxa with large seeds and simple leaves. This information can help to enhance our understanding of forest responses to past environmental changes, and improve predictions of future changes in tropical forest composition.     

Diet analysis by next‐generation sequencing indicates the frequent consumption of introduced plants by the critically endangered red‐headed wood pigeon (Columba janthina nitens) in oceanic island habitats

Oceanic island ecosystems are vulnerable to the introduction of alien species, and they provide a habitat for many endangered species. Knowing the diet of an endangered animal is important for appropriate nature restoration efforts on oceanic islands because introduced species may be a major component of the diets of some endangered species. DNA barcoding techniques together with next‐generation sequencing may provide more detailed information on animal diets than other traditional methods. We performed a diet analysis using 48 fecal samples from the critically endangered red‐headed wood pigeon that is endemic to the Ogasawara Islands based on chloroplast trnL P6 loop sequences. The frequency of each detected plant taxa was compared with a microhistological analysis of the same sample set. The DNA barcoding approach detected a much larger number of plants than the microhistological analysis. Plants that were difficult to identify by microhistological analysis after being digested in the pigeon stomachs were frequently identified only by DNA barcoding. The results of the barcoding analysis indicated the frequent consumption of introduced species, in addition to several native species, by the red‐headed wood pigeon. The rapid eradication of specific introduced species may reduce the food resources available to this endangered bird; thus, balancing eradication efforts with the restoration of native food plants should be considered. Although some technical problems still exist, the trnL approach to next‐generation sequencing may contribute to a better understanding of oceanic island ecosystems and their conservation.     

Trophic niche,capture efficiency and venom profiles of six sympatric ant‐eating spider species (Araneae: Zodariidae)

The arms race between specialist predators and their prey has resulted in the evolution of a variety of specific adaptations. In venomous predators, this can include venom composition, particularly if predators are specialized on dangerous prey. Here, we performed an integrative study using six species of highly specialized ant‐eating spiders of the genus Zodarion to investigate their phylogeny, realized trophic niche, efficacy in the capture of various ant species and venom composition. Data on natural diet obtained by next‐generation sequencing and field observations showed that the six Zodarion species exploit different ant species. Their phylogeny, based on mitochondrial and nuclear genes, correlated with the composition of their natural prey, indicating that closely related Zodarion species specialize on similar ant species. Prey‐capture parameters differed among Zodarion species suggesting prey‐specific efficacy. Similarly, the venom profiles of both low and high molecular compounds differed among species. Only the profiles of low molecular compounds were correlated with capture efficacy parameters, suggesting that the venom of Zodarion spiders contains prey‐specific components. Our study suggests that Iberian Zodarion spiders are specialized on particular ant species.     

Archolaemus janeae (Gymnotiformes,Teleostei): First insights into karyotype and repetitive DNA distribution in two populations of the Amazon

Archolaemus, one of the five genera of Neotropical freshwater fish of the family Sternopygidae (Gymnotiformes), was long considered a monotypic genus represented by Archolaemus blax. Currently, it consists of six species, most of them occurring in the Amazon region. There are no cytogenetic data for species of this genus. In the present study, we used classical cytogenetics (conventional staining and C‐banding) and molecular cytogenetics (probes of telomeric sequences and multigenic families 18S rDNA, 5S rDNA, and U2 snDNA) to study the karyotype of Archolaemus janeae from Xingu and Tapajós rivers in the state of Pará (Brazil). The results showed that the two populations have identical karyotypes with 46 chromosomes: four submetacentric and 42 acrocentric (2n = 46; 4m/sm + 42a). Constitutive heterochromatin occurs in the centromeric region of all chromosomes, in addition to small bands in the interstitial and distal regions of some pairs. The 18S rDNA occurs in the distal region of the short arm of pair 2; the 5S rDNA occurs in five chromosome pairs; and the U2 snDNA sequence occurs in chromosome pairs 3, 6, and 13. No interstitial telomeric sequence was observed. These results show karyotypic similarity between the studied populations suggesting the existence of a single species and are of great importance as a reference for future cytotaxonomic studies of the genus.