Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing

Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere.

Long-Term Effects of Soil Remediation with Willow Short Rotation Coppice on Biogeographic Pattern of Microbial Functional Genes

Short rotation coppice (SRC) is increasingly being adopted for bioenergy production, pollution remediation and land restoration. However, its long-term effects on soil microbial communities are poorly characterized. Here, we studied soil microbial functional genes and their biogeographic pattern under SRC with willow trees as compared to those under permanent grassland (C). GeoChip analysis showed a lower functional gene diversity in SRC than in C soil, whereas microbial ATP and respiration did not change. The SRC soil had lower relative abundances of microbial genes encoding for metal(-oid) resistance, antibiotic resistance and stress-related proteins. This indicates a more benign habitat under SRC for microbial communities after relieving heavy metal stress, consistent with the lower phytoavailability of some metals (i.e., As, Cd, Ni and Zn) and higher total organic carbon, NO3−-N and P concentrations. The microbial taxa–area relationship was valid in both soils, but the space turnover rate was higher under SRC within 0.125 m2, which was possibly linked to a more benign environment under SRC, whereas similar values were reached beyond thisarea. Overall, we concluded that SRC management can be considered as a phytotechnology that ameliorates the habitat for soil microorganisms, owing to TOC and nutrient enrichment on the long-term.

Community structure of benthic invertebrates in the Allipén River basin, North Patagonia, Araucania region (38º S, Chile)

One of the biological indicators most used to determine the health of a fluvial ecosystem are the benthic macroinvertebrates. The presence of recurrent species in a wide gradient of latitudes, dominates the biogeographic pattern of the benthic macroinvertebrates in Chilean fresh waters, nevertheless the knowledge on the communitarian ecology of these in the Chilean rivers continues to be scarce. Null models became a powerful statistical tool for describing the ecological mechanisms that drive the structure of an ecological community and the underlying patterns of diversity. The objective of this study was to determine the community structure of benthic invertebrates in the Allipén River by describing their composition, richness and abundance of species through richness models and null models based on presence/absence. The results reveal a high family richness and low diversity, three phyla, five classes, 11 orders and 28 families were identified in the study area during the four seasons of the year. The Arthropoda phylum was the most representative in abundance and richness. Regarding to richness, Trichoptera (7 families) and Diptera (6 families) followed by Ephemeroptera (3 families) were the orders that showed the greatest diversity of families, however, a low diversity with a H’≤ 1.5 nit was registered in the study area. We demonstrated through the null models, the randomization in the species associations corresponding to the three analyzed sites. The information provided here contributes to the understanding of the ecological patterns of the invertebrate communities in the Allipén River, establishing the basis for more complex ecological studies.

New Remains of Scandiavis mikkelseni Inform Avian Phylogenetic Relationships and Brain Evolution

Although an increasing number of studies are combining skeletal and neural morphology data in a phylogenetic context, most studies do not include extinct taxa due to the rarity of preserved endocasts. The early Eocene avifauna of the Fur Formation of Denmark presents an excellent opportunity for further study of extinct osteological and endocranial morphology as fossils are often exceptionally preserved in three dimensions. Here, we use X-ray computed tomography to present additional material of the previously described taxon Scandiavis mikkelseni and reassess its phylogenetic placement using a previously published dataset. The new specimen provides novel insights into the osteological morphology and brain anatomy of Scandiavis. The virtual endocast exhibits a morphology comparable to that of modern avian species. Endocranial evaluation shows that it was remarkably similar to that of certain extant Charadriiformes, yet also possessed a novel combination of traits. This may mean that traits previously proposed to be the result of shifts in ecology later in the evolutionary history of Charadriiformes may instead show a more complex distribution in stem Charadriiformes and/or Gruiformes depending on the interrelationships of these important clades. Evaluation of skeletal and endocranial character state changes within a previously published phylogeny confirms both S. mikkelseni and a putative extinct charadriiform, Nahmavis grandei, as charadriiform. Results bolster the likelihood that both taxa are critical fossils for divergence dating and highlight a biogeographic pattern similar to that of Gruiformes.

Metagenomic analysis of Raphidiopsis raciborskii microbiome: beyond the individual

Raphidiopsis raciborskii is a toxic, invasive bacteria with a defined biogeographic pattern attributed to the generation of ecotypes subjected to local environmental filters and to phenotypic plasticity. The interactions taking place between the cyanobacterium and the other bacteria inhabiting the external polysaccharide-rich matrix surrounding the cells, or phycosphere, may be ecotype-specific and would have different influence on the carbon and nutrient cycling in the ecosystem. Here, we describe the bacterial community or microbiome (assessed by 16S rRNA metagenomics) associated to two R. raciborskii strains that have been described as different ecotypes: the saxitoxin-producer MVCC19 and the non-toxic LB2897. Our results showed that both ecotypes share 50% of their microbiomes and differ in their dominant taxa. The taxon having the highest abundance in the microbiome of MVCC19 was Neorhizobium (22.5% relative abundance), while the dominant taxon in LB2897 was the Planctomycetes SM1A02 (26.2% relative abundance). These groups exhibit different metabolic capabilities regarding nitrogen acquisition (symbiotic nitrogen-fixing in Neorhizobium vs. anammox in SM1A02), suggesting the existence of ecotype-specific microbiomes that play a relevant role in cyanobacterial niche-adaptation. In addition, as saxitoxin and analogues are nitrogen-rich (7 atoms per molecule), we hypothesise that saxitoxin-producing R. raciborskii benefits from external sources of nitrogen provided by the microbiome bacteria. Based on these findings, we propose that the mechanisms involved in the assembly of the cyanobacterial microbiome community are ecotype-dependent.

Evolution and phylogeny of the deep-sea isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 (Isopoda: Asellota)

In the deep sea, the phylogeny and biogeography of only a few taxa have been well studied. Although more than 200 species in 32 genera have been described for the asellote isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 from all ocean basins, their phylogenetic relationships are not completely understood. There is little doubt about the close relationship of these families, but the taxonomic position of a number of genera is so far unknown. Based on a combined morphological phylogeny using the Hennigian method with a dataset of 107 described species and a molecular phylogeny based on three markers (COI, 16S, and 18S) with 75 species (most new to science), we could separate Desmosomatidae and Nannoniscidae as separate families. However, we could not support the concept of the subfamilies Eugerdellatinae Hessler, 1970 and Desmosomatinae Hessler, 1970. Most genera of both families were well supported, but several genera appear as para- or even polyphyletic. Within both families, convergent evolution and analogies caused difficulty in defining apomorphies for phylogenetic reconstructions and this is reflected in the results of the concatenated molecular tree. There is no biogeographic pattern in the distribution as the genera occur over the entire Atlantic and Pacific Ocean, showing no specific phylogeographical pattern. Poor resolution at deep desmosomatid nodes may reflect the long evolutionary history of the family and rapid evolutionary radiations.

High biogeographic and latitudinal variability in gastropod drilling predation on molluscs along the eastern Indian coast: Implications on the history of fossil record of drillholes

Studies on the large-scale latitudinal patterns of gastropod drilling predation reveal that predation pressure may decrease or increase with increasing latitude, or even show no trend, questioning the generality of any large-scale latitudinal or biogeographic pattern. Here, we analyze the nature of spatio-environmental and latitudinal variation in gastropod drilling along the Indian eastern coast by using 76 samples collected from 39 locations, covering ~2500 km, incorporating several ecoregions, and ~15° latitudinal extents. We find no environmental or latitudinal gradient. In fact, drilling intensity varies highly within the same latitudinal bin, or oceanic sub-basins, or even the same ecoregions. Moreover, different ecoregions with their distinctive biotic and abiotic environmental variables show similar predation intensities. However, one pattern is prevalent: some small infaunal prey taxa, living in the sandy-muddy substrate—which are preferred by the naticid gastropods—are always attacked more frequently over others, indicating taxon and size selectivity by the predators. The result suggests that the biotic and abiotic factors, known to influence drilling predation, determine only the local predation pattern. In the present case, the nature of substrate and prey composition determines the local predation intensity: soft substrate habitats host dominantly small, infaunal prey. Since the degree of spatial variability in drilling intensity within any time bin can be extremely high, sometimes greater than the variability across consecutive time bins, temporal patterns in drilling predation can never be interpreted without having detailed knowledge of the nature of this spatial variability within a time bin.

Biogeography of Italy revisited: genetic lineages confirm major phylogeographic patterns and a pre-Pleistocene origin of its biota

Warm-adapted species survived the cold stages of the past glacial-interglacial cycles in southern European peninsulas and recolonized major parts of Central and Northern Europe in the wake of postglacial warming. However, many of the genetic lineages which differentiated within these refugia predate even the Pleistocene. One of these refugia is the Italian Peninsula with its surrounding islands. In this meta-analysis, we compiled phylogeographic patterns of multiple species across this region. We transformed existing geographic information on 78 animal and plant species (with a total of 471 genetic lineages) within 17 predefined areas into presence/absence matrices. We elaborated three matrices: (i) only old lineages exclusively distinguished by deep splits, (ii) only young lineages distinguished by shallow (i.e. recent) splits, and (iii) presence/absence of the respective species. To infer biogeographic relationships between the predefined areas, we performed bootstrapped neighbour joining cluster analyses on these three matrices. In addition, we reviewed the geological history of Italy to identify causes of the observed biogeographic patterns. We found Sardinia and Corsica to be biogeographically closely linked with each other, and that they diverge strongly from all other regions. Sicily also diverges strongly from all other regions, while the intra-island differentiation was comparatively low. On the Italian mainland, Calabria exhibited the most pronounced biogeographic differentiation, often with several lineages present, resulting from old vicariance events within the region. Furthermore, southern Apulia and the Po Plain with adjoining areas of northern peninsular Italy displayed considerable distinctiveness. Admixture prevailed in the areas between these three regions. The ancient isolation of Sicily, as well as Sardinia plus Corsica, resulted in endemic lineages with only moderate recent exchange with adjacent mainland regions. Pronounced diversification occurs within the Italian Peninsula. The complex tectonic activities, such as shifting (micro)plates, submergence of major parts of peninsular Italy with the genesis of numerous Pliocene islands, in combination with the climatic cycles during the Pleistocene have most likely generated the current biogeographic pattern of species. Immigrations from the Balkan Peninsula into northern Italy partly accounted for the distinctiveness of this region.

Biogeographic Overview of Ulmaceae: Diversity, Distribution, Ecological Preferences, and Conservation Status

The elm family (Ulmaceae) is a woody plant group with important scientific, societal, and economic value. We aim to present the first biogeographic synthesis investigating the global diversity, distribution, ecological preferences, and the conservation status of Ulmaceae. A literature review was performed to explore the available data for all extant species. Our study made it possible to map the actual global distribution of Ulmaceae with high precision, and to elucidate the centers of diversity, located mainly in China and in the southeastern USA. A detailed comparative analysis of the macroclimatic niche for each species was produced, which shows the general biogeographic pattern of the family and pinpoints the outlier species. The results corroborate recent molecular analyses and support the division of Ulmaceae into two taxonomically, biogeographically, and ecologically well-differentiated groups: the so-called temperate clade with 4 genera and 43 species and the tropical clade with 3 genera and 13 species. The elm family is often described as a typical temperate plant group, however the diversity peak of all Ulmaceae is located in the subtropical zone, and a non-negligible part of the family is exclusively distributed in the tropics. We also noticed that a high proportion of Ulmaceae is linked to humid macro- or microhabitats. Finally, we highlighted that nearly 25% of all Ulmaceae are threatened. Fieldwork, conservation efforts, and research activities are still necessary for this family, particularly for the tropical members and the most endangered species.