Substrate Generalist Research Articles

Neospongodes atlantica, a potential case of an early biological introduction in the Southwestern Atlantic.

Soft corals (Anthozoa: Octocorallia) are discreet components in the Southwestern Atlantic reef communities. In Brazil, the native octocoral shallow-reef fauna is mostly represented by gorgonians. Consequently, except for the nephtheid Neospongodes atlantica, most of the known soft corals from this region are considered non-indigenous. Hitherto, the monotypic genus Neospongodes, which was proposed in the early 1900s, has been considered to be endemic to the Northeastern Brazilian coast. Herein, based on in situ records, we show that N. atlantica is a substrate generalist that has been probably expanding its distribution by dominating extensive shallow and mesophotic sandy and reef bottoms, generally outcompeting other reef benthic organisms, including Brazilian endemic species. Based on previously unidentified museum specimens, new records, and a broad literature review, we provide the most comprehensive modelling of the potential distribution of this species in the Southwestern Atlantic. Based on molecular inference supported by in-depth morphological analysis, the probable non-indigenous and, therefore, ancient introduction of N. atlantica in Brazilian waters is discussed. Finally, these results support that Neospongodes and the Indo-Pacific Stereonephthya are synonyms, which led us to propose the latter as taxonomically invalid.

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes.

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

Succession of Microbial Decomposers Is Determined by Litter Type, but Site Conditions Drive Decomposition Rates.

Soil microorganisms are diverse, although they share functions during the decomposition of organic matter. Thus, preferences for soil conditions and litter quality were explored to understand their niche partitioning. A 1-year-long litterbag transplant experiment evaluated how soil physicochemical traits of contrasting sites combined with chemically distinct litters of sedge (S), milkvetch (M) from a grassland, and beech (B) from forest site decomposition. Litter was assessed by mass loss; C, N, and P contents; and low-molecular-weight compounds. Decomposition was described by the succession of fungi, Actinobacteria, Alphaproteobacteria, and Firmicutes; bacterial diversity; and extracellular enzyme activities. The M litter decomposed faster at the nutrient-poor forest site, where the extracellular enzymes were more active, but microbial decomposers were not more abundant. Actinobacteria abundance was affected by site, while Firmicutes and fungi by litter type and Alphaproteobacteria by both factors. Actinobacteria were characterized as late-stage substrate generalists, while fungi were recognized as substrate specialists and site generalists, particularly in the grassland. Overall, soil conditions determined the decomposition rates in the grassland and forest, but successional patterns of the main decomposers (fungi and Actinobacteria) were determined by litter type. These results suggest that shifts in vegetation mostly affect microbial decomposer community composition.IMPORTANCE Anthropogenic disturbance may cause shifts in vegetation and alter the litter input. We studied the decomposition of different litter types under soil conditions of a nutrient-rich grassland and nutrient-poor forest to identify factors responsible for changes in the community structure and succession of microbial decomposers. This will help to predict the consequences of induced changes on the abundance and activity of microbial decomposers and recognize if the decomposition process and resulting quality and quantity of soil organic matter will be affected at various sites.

The evolution of fungal substrate specificity in a widespread group of crustose lichens.

Lichens exhibit varying degrees of specialization with regard to the surfaces they colonize, ranging from substrate generalists to strict substrate specialists. Though long recognized, the causes and consequences of substrate specialization are poorly known. Using a phylogeny of a 150–200 Mya clade of lichen fungi, we asked whether substrate niche is phylogenetically conserved, which substrates are ancestral, whether specialists arise from generalists or vice versa and how specialization affects speciation/extinction processes. We found strong phylogenetic signal for niche conservatism. Specialists evolved into generalists and back again, but transitions from generalism to specialism were more common than the reverse. Our models suggest that for this group of fungi, ‘escape’ from specialization for soil, rock and bark occurred, but specialization for wood foreclosed evolution away from that substrate type. In parallel, speciation models showed positive diversification rates for soil and rock dwellers but not other specialists. Patterns in the studied group suggest that fungal substrate specificity is a key determinant of evolutionary trajectory for the entire lichen symbiosis.

Benthic hydroids (Cnidaria, Hydrozoa) from Alacranes Reef, Gulf of Mexico, Mexico

Here, we provide the first list of shallow-water hydroids for Alacranes Reef, Mexico, comprising 49 species in 33 genera. The most speciose superorder was Leptothecata (36 species), with three particularly diverse families: Clytiidae, Sertulariidae, and Plumulariidae. Three species were recorded for the first time in the Gulf of Mexico (GoM), and 13 for the south-central GoM. The majority of fauna was substrate generalist with specific distributions: 38 hydroid species occurred on natural reefs, 18 on artificial reefs, 9 on drifting Sargassum spp., and 8 on the seagrass Thalassia testudinum K.D. Koenig. Our results significantly increase knowledge of the hydroids from Mexican waters. This is an important step toward detecting non-native species in the near future, as well as for improving and designing new conservation programs in the area.

Short-Term Dynamics of North Sea Bacterioplankton-Dissolved Organic Matter Coherence on Molecular Level.

Remineralization and transformation of dissolved organic matter (DOM) by marine microbes shape the DOM composition and thus, have large impact on global carbon and nutrient cycling. However, information on bacterioplankton-DOM interactions on a molecular level is limited. We examined the variation of bacterial community composition (BCC) at Helgoland Roads (North Sea) in relation to variation of molecular DOM composition and various environmental parameters on short-time scales. Surface water samples were taken daily over a period of 20 days. Bacterial community and molecular DOM composition were assessed via 16S rRNA gene tag sequencing and ultrahigh resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), respectively. Environmental conditions were driven by a coastal water influx during the first half of the sampling period and the onset of a summer phytoplankton bloom toward the end of the sampling period. These phenomena led to a distinct grouping of bacterial communities and DOM composition which was particularly influenced by total dissolved nitrogen (TDN) concentration, temperature, and salinity, as revealed by distance-based linear regression analyses. Bacterioplankton-DOM interaction was demonstrated in strong correlations between specific bacterial taxa and particular DOM molecules, thus, suggesting potential specialization on particular substrates. We propose that a combination of high resolution techniques, as used in this study, may provide substantial information on substrate generalists and specialists and thus, contribute to prediction of BCC variation.

Similiclava nivea (Cnidaria: Hydrozoa: Similiclavidae): a new family, genus and species of athecate hydroid from the Pacific coast of North America

The hydroid Similiclava nivea, gen. nov., sp. nov., is described from colonies collected in nearshore waters of southern British Columbia, Canada. It has been observed by divers, and recorded as Clava sp., several hundred times at locations between southeast Alaska and southern Oregon, USA. While resembling the hydractiniid Clava multicornis, tentacles of S. nivea are arranged in two close whorls in extended hydranths rather than being scattered over the distal end of the hydranth. Moreover, the hypostome is dome-shaped to flattened instead of being proboscidiform. Similiclava nivea also resembles species of the hydractiniid genera Stylactaria, Hydractinia and Podocoryna, but differs in being monomorphic, in lacking spines on the hydrorhiza and in having numerous (as many as 50 or more) sporosacs borne in a broad whorl below the tentacles on normal hydranths. Molecular analysis using the mitochondrial 16S gene sequences reveals that S. nivea is closer to Clathrozoellidae than to Hydractiniidae, although it is clearly distinct from both. A new family, Similiclavidae, is established to accommodate the species. Hydroids of S. nivea were observed at relatively shallow depths (10–30 m) on rocks and epibiota attached to rocky substrates. Colonies are conspicuous because of the relatively large surface area they occupy (up to 20 cm across, and in aggregations often exceeding 100 or more hydranths) together with the height (about 15 mm high when extended) and striking white colour of living hydranths. The cnidome consists of desmonemes, microbasic euryteles and microbasic mastigophores. A substrate generalist observed on rocks, algae, sponges, barnacles, bryozoans and other hydroids in cold-temperate waters, S. nivea is most prevalent in shallow subtidal areas swept by tidal currents.http://zoobank.org/urn:lsid:zoobank.org:pub:2691E02E-7E14-4820-8D91-41D9E7E8BF62

Genetic consequences of postglacial range expansion in two codistributed rodents (genus Dipodomys) depend on ecology and genetic locus.

How does range expansion affect genetic diversity in species with different ecologies, and do different types of genetic markers lead to different conclusions? We addressed these questions by assessing the genetic consequences of postglacial range expansion using mitochondrial DNA (mtDNA) and nuclear restriction site-associated DNA (RAD) sequencing in two congeneric and codistributed rodents with different ecological characteristics: the desert kangaroo rat (Dipodomys deserti), a sand specialist, and the Merriam's kangaroo rat (Dipodomys merriami), a substrate generalist. For each species, we compared genetic variation between populations that retained stable distributions throughout glacial periods and those inferred to have expanded since the last glacial maximum. Our results suggest that expanded populations of both species experienced a loss of private mtDNA haplotypes and differentiation among populations, as well as a loss of nuclear single-nucleotide polymorphism (SNP) private alleles and polymorphic loci. However, only D.deserti experienced a loss of nucleotide diversity (both mtDNA and nuclear) and nuclear heterozygosity. For all indices of diversity and differentiation that showed reduced values in the expanded areas, D.deserti populations experienced a greater degree of loss than did D.merriami populations. Additionally, patterns of loss in genetic diversity in expanded populations were substantially less extreme (by two orders of magnitude in some cases) for nuclear SNPs in both species compared to that observed for mitochondrial data. Our results demonstrate that ecological characteristics may play a role in determining genetic variation associated with range expansions, yet mtDNA diversity loss is not necessarily accompanied by a matched magnitude of loss in nuclear diversity.

The evolution of substrate differentiation in Minuartia series Laricifoliae (Caryophyllaceae) in the European Alps: In situ origin or repeated colonization?

Substrate specialization is often considered an important factor in evolutionary diversification. A classic example of divergence related to different substrate types is the dichotomy between calcicole and calcifuge plants on calcareous and siliceous substrates as found in the European Alps. When closely related species with contrasting substrate preferences are found in the same area, it is generally hypothesized that they diverged where they now occur. However, it is possible that Alpine edaphic diversity instead allows the coexistence of related species whose edaphic differentiation took place deeper in the phylogeny, in some other part of the range of their clades. We used sequences of the nuclear internal and external transcribed spacer regions to examine the origin of substrate differentiation in Minuartia series Laricifoliae, which contains many edaphic endemics, including a pair of Alpine taxa with contrasting substrate preferences: Minuartia langii (calcicole) and M. laricifolia (calcifuge). MINUARTIA LANGII and M. laricifolia are each more closely related to Balkan species than they are to each other and reached the Alps independently. The clade to which they belong is ancestrally calcicole. Minuartia langii inherited the ancestral ecology, while M. laricifolia is part of a subclade with serpentine endemics and one substrate generalist. In the study group, taxa with contrasting substrate preferences did not diverge in the Alps. Instead, taxa whose substrate differentiation arose elsewhere, likely on the Balkan Peninsula, were preadapted to take advantage of Alpine substrate diversity.

Diversity of Meiofauna from the 9°50′N East Pacific Rise across a Gradient of Hydrothermal Fluid Emissions

BackgroundWe studied the meiofauna community at deep-sea hydrothermal vents along a gradient of vent fluid emissions in the axial summit trought (AST) of the East Pacific Rise 9°50′N region. The gradient ranged from extreme high temperatures, high sulfide concentrations, and low pH at sulfide chimneys to ambient deep-sea water conditions on bare basalt. We explore meiofauna diversity and abundance, and discuss its possible underlying ecological and evolutionary processes.Methodology/Principal FindingsAfter sampling in five physico-chemically different habitats, the meiofauna was sorted, counted and classified. Abundances were low at all sites. A total of 52 species were identified at vent habitats. The vent community was dominated by hard substrate generalists that also lived on bare basalt at ambient deep-sea temperature in the axial summit trough (AST generalists). Some vent species were restricted to a specific vent habitat (vent specialists), but others occurred over a wide range of physico-chemical conditions (vent generalists). Additionally, 35 species were only found on cold bare basalt (basalt specialists). At vent sites, species richness and diversity clearly increased with decreasing influence of vent fluid emissions from extreme flow sulfide chimney (no fauna), high flow pompei worm (S: 4–7, H'loge: 0.11–0.45), vigorous flow tubeworm (S: 8–23; H'loge: 0.44–2.00) to low flow mussel habitats (S: 28–31; H'loge: 2.34–2.60).Conclusions/SignificanceOur data suggest that with increasing temperature and toxic hydrogen sulfide concentrations and increasing amplitude of variation of these factors, fewer species are able to cope with these extreme conditions. This results in less diverse communities in more extreme habitats. The finding of many species being present at sites with and without vent fluid emissions points to a non endemic deep-sea hydrothermal vent meiofaunal community. This is in contrast to a mostly endemic macrofauna but similar to what is known for meiofauna from shallow-water vents.

Local spatial pattern in the occurrence of two congeneric wood-decaying fungi in an old-growth boreal forest

This paper characterizes spatial patterns in the occurrence of two congeneric wood-decaying fungi (Aphyllophorales: Polyporaceae) in an old-growth boreal forest in eastern Finland. The spatial patterns are used to evaluate indirectly the short-distance dispersal ability of the species. Fomitopsis rosea is a specialist on Picea abies occurring mainly in forests with large amounts of dead wood, whereas Fomitopsis pinicola is a substrate generalist and also abundant in managed forests. Within a forest reserve, a 25 ha study area was divided into 25 m×25 m grid (n=400), and all dead trees and fruiting bodies of the two polypore species were recorded. Spatial patterns were analysed with Spatial Analysis by Distance IndicEs methodology (SADIE). Downed spruce logs were highly aggregated within the study area. After this distribution was accounted for, the spatial pattern of F. pinicola and F. rosea on logs was random. The lack of spatial aggregation suggests that within old-growth forest stands dispersal of the two fungal species is not a limiting factor for their occurrence.

Differences between epilithic and epizoic hydroid assemblages from commercial scallop grounds in the Bay of Fundy, northwest Atlantic

Hydroid assemblages from the shells of 104 live scallops Placopecten magellanicus and 136 cobbles were sampled from 39 sites on heavily dredged commercial scallop grounds in the Bay of Fundy, northwest Atlantic. The scallop shells were considered pseudo-controls, representing undisturbed 'island habitats' naturally interspersed amongst the cobbles. Cobbles were expected to represent disturbed habitat. Samples yielded 51 taxa from 24 genera across substrata. The number of taxa was significantly lower on cobbles. Multidimensional scaling plots and statistical analyses on presence-absence data discriminated 2 divergent assemblages consistent with substratum. Cobble assemblages were characterized by Campanularia volubilis, Clytia hemisphaerica and Clytia sp., while those on the live scallop shells were characterized by the small auto-epizoite Calycella syringa and its hosts Sertularia cupressina and Obelia dichotoma. Species discriminating between the sub- strata are considered substrate generalists. Fishing effort was introduced as a factor in an analysis of similarity and accounted for a significant proportion of the variance within and between substrata, with larger R 2 values associated with the cobble assemblages, as expected. Runner-like forms with small, unbranched colonies and medusa life stages were more frequently found on cobbles than on live scallop shells. Assemblage and life history divergence associated with fishing effort, widespread substrate generalism amongst the principle taxa, and observations from other studies suggest that these observed differences could be related to chronic disturbance of cobbles caused by fishing.

BURROWING AND SWASH BEHAVIOR OF THE PACIFIC MOLE CRAB HIPPA PACIFICA (ANOMURA, HIPPIDAE) IN TROPICAL SANDY BEACHES

To investigate factors associated with the distribution of an intertidal crab, Hippa pacifica Dana, which is common in the swash zones of reflective subtropical and tropical sandy beaches, we examined the effect of sediment size on burrowing rates of a wide size range of individuals. We also examined aspects of swash behavior in field conditions, including drift time, distance and velocity of individual crabs. Hippa pacifica burrowed very rapidly (in 0.3 to 2.7 s) in laboratory and field conditions. Burrowing time increased significantly with increasing crab size in all sediments tested but did not differ between male and female crabs nor between ovigerous and non-ovigerous crabs. There were no significant differences in burrowing times among five sediments ranging from very fine sand to gravel, suggesting that this species is a sediment generalist whose distribution is not limited by sediment size. Individual crabs released in the swash zone of a reflective beach oriented, swam and/or drifted for 1.2 to 3.8 seconds before contacting substrate and burrowing. Drift times were similar for all sizes of crabs. However, drift distance (ranging 0.10 m to 1.16 m) and drift velocity (ranging 0.11 m/s to 0.45 m/s), decreased with increasing crab size, suggesting a possible mechanism for size-specific zonation patterns reported in this species. Burrowing times observed in H. pacifica in this study were faster than reported for other sandy beach macrofauna, including tropical forms. This burrowing ability, in combination with the characteristics of substrate generalist and well-oriented swash behavior, appear to be a key to the ability of H. pacifica to inhabit reflective coarse sand beaches.

Burrowing and Swash Behavior of the Pacific Mole Crab Hippa Pacifica (Anomura, Hippidae) in Tropical Sandy Beaches

To investigate factors associated with the distribution of an intertidal crab, Hippa pacifica Dana, which is common in the swash zones of reflective subtropical and tropical sandy beaches, we examined the effect of sediment size on burrowing rates of a wide size range of individuals. We also examined aspects of swash behavior in field conditions, including drift time, distance and velocity of individual crabs. Hippa pacifica burrowed very rapidly (in 0.3 to 2.7 s) in laboratory and field conditions. Burrowing time increased significantly with increasing crab size in all sediments tested but did not differ between male and female crabs nor between ovigerous and non-ovigerous crabs. There were no significant differences in burrowing times among five sediments ranging from very fine sand to gravel, suggesting that this species is a sediment generalist whose distribution is not limited by sediment size. Individual crabs released in the swash zone of a reflective beach oriented, swam and/or drifted for 1.2 to 3.8 seconds before contacting substrate and burrowing. Drift times were similar for all sizes of crabs. However, drift distance (ranging 0.10 m to 1.16 m) and drift velocity (ranging 0.11 m/s to 0.45 m/s), decreased with increasing crab size, suggesting a possible mechanism for size-specific zonation patterns reported in this species. Burrowing times observed in H. pacifica in this study were faster than reported for other sandy beach macrofauna, including tropical forms. This burrowing ability, in combination with the characteristics of substrate generalist and well-oriented swash behavior, appear to be a key to the ability of H. pacifica to inhabit reflective coarse sand beaches.

Burrowing abilities and swash behavior of three crabs, Emerita analoga Stimpson, Blepharipoda occidentalis Randall, and Lepidopa californica Efford (Anomura, Hippoidea), of exposed sandy beaches.

To investigate factors related to the distribution of intertidal species, and specific predictions of the swash exclusion hypothesis for exposed sandy beaches, we compared the burrowing abilities and swash behavior of three species of anomuran crabs in the superfamily Hippoidea (Emerita analoga, Blepharipoda occidentalis and Lepidopa californica) which commonly inhabit the intertidal and shallow subtidal zones of beaches along the California coast. Burrowing times in the laboratory increased significantly with crab size for all species in five sediment grain sizes ranging from fine sand to gravel (0.15 to 3.24 mm). For each species, burrowing times differed significantly among sand grain sizes, ranging from 0.3 to 21.5 s. Burrowing times for the hippid crab, E. analoga, were relatively constant across sediment types, while those of the albuneid crabs, B. occidentalis and L. californica, were rapid in fine to medium sands, and much slower in coarser sediments. Our results indicate that E. analoga is a substrate generalist while L. californica and B. occidentalis are substrate sensitive. Pre-burrowing times and behavior, distance moved, and burrowing times differed among the species in the swash zone. Combined times of preburrowing and burrowing were shorter than the swash period (6 s) for most E. analoga individuals. Fifty percent of the individuals of L. californica reached the substrate and burrowed in the swash period, while no individuals of B. occidentalis burrowed in that time. Pre-burrowing behavior and time may be valuable in explaining spatial and temporal patterns in the distribution of hippoid crabs on California beaches. Our results support predictions of the swash exclusion hypothesis concerning the burrowing and locomotory abilities of sandy beach macrofauna. The substrate generalist characteristics, and unique orientation and swimming abilities of the hippid crab, E. analoga, in intertidal swash may help explain the success of this species and its congeners, and have important implications for understanding patterns of macrofauna community structure on exposed sandy beaches in California and other regions.

Influence of Sediment Grain Size on the Burrowing of Bivalves: Correlation with Distribution and Stratigraphic Persistence of Selected Neogene Clams

Burrowing ability of 21 species of clams from Oregon, New Jersey, and Scotland was determined in each sieved sediment ranging from fine gravel to mud in half phi increments. A burrowing rate index (BRI), which normalizes burrowing time for specimen mass, was calculated for each species in each sediment. Skewness and kurtosis of the profile of average BRI's across the range of grain sizes was used to categorize species as substrate generalists, substrate sensitive, or substrate specialists. Substrate generalists (Anadara ovalis, Mercenaria mercenaria, Astarte sulcata, Venerupis decussata, Venus striatula, Venus casina, Mya arenaria] burrowed slowly into a wide range of grain sizes

Diet selection in Amazonian antwrens: consequences of substrate specialization

I used an observational and experimental approach to investigate the dietary consequences of substrate specialization in six species of Amazonian antwrens (Myrmotherula). Three species (leucophthalma, haematonota, and ornata) foraged exclusively at curled dead leaves suspended above ground, axillaris and longipennis foraged on live foliage, and hauxwelli was a substrate generalist, feeding at both live and dead foliage. Diet composition of all species was qualitatively similar, with soft-bodied orthopterans consistently the most important prey type. Dead-leaf specialists took other prey roughly in proportion to their availability in dead leaves, whereas diets of live-leaf foragers differed greatly from prey available on live foliage. Dead-leaf specialists also ate larger prey and especially larger orthopterans than did other antwrens. Substrate generalization in hauxwelli was associated with higher diet breadth and greater heterogeneity among individuals, compared with substrate-restricted foragers. Diet breadth was negatively correlated with prey size across all six species. When tested in outdoor cages, live-leaf foraging and generalist species showed little interest in dead- or live-leaf substrates, whereas all dead-leafers repeatedly inspected and manipulated dead and curled leaves in the absence of food. All foraging groups showed a similar degree of selectivity of prey types in feeding trials. Dead-leaf specialists did not differ from other species in their preference for orthopterans of different colors, although specialists were better able to catch and handle the largest katydids (>30 mm). Individual hauxwelli (the generalist) showed elevated levels of exploration at dead leaves with food reinforcement, suggesting short-term plasticity in search behavior. I conclude that substrate specialization in these birds involves fundamental differences in search behavior, but is not accompanied by equivalent changes in prey selectivity or preference. Dead-leaf specialists search for suitable substrates and then inspect them for hidden prey, taking prey roughly in proportion to their availability. In contrast live-leaf foragers search directly for prey and select suitable items from the wider array of arthropods available on live foliage. Substrate-restricted foraging may reduce diet breadth and promote diet stereotypy in both groups, whereas the single most important factor promoting specialization on dead leaves may be the predictable abundance of relatively large orthopterans. Received 25 November 1991, accepted 27 May 1992.