Mycoplasma leachii sp. nov. as a new species designation for Mycoplasma sp. bovine group 7 of Leach, and reclassification of Mycoplasma mycoides subsp. mycoides LC as a serovar of Mycoplasma mycoides subsp. capri

The Mycoplasma mycoides cluster consists of six pathogenic mycoplasmas causing disease in ruminants, which share many genotypic and phenotypic traits. The M. mycoides cluster comprises five recognized taxa: Mycoplasma mycoides subsp. mycoides Small Colony (MmmSC), M. mycoides subsp. mycoides Large Colony (MmmLC), M. mycoides subsp. capri (Mmc), Mycoplasma capricolum subsp. capricolum (Mcc) and M. capricolum subsp. capripneumoniae (Mccp). The group of strains known as Mycoplasma sp. bovine group 7 of Leach (MBG7) has remained unassigned, due to conflicting data obtained by different classification methods. In the present paper, all available data, including recent phylogenetic analyses, have been reviewed, resulting in a proposal for an emended taxonomy of this cluster: (i) the MBG7 strains, although related phylogenetically to M. capricolum, hold sufficient characteristic traits to be assigned as a separate species, i.e. Mycoplasma leachii sp. nov. (type strain, PG50(T) = N29(T) = NCTC 10133(T) = DSM 21131(T)); (ii) MmmLC and Mmc, which can only be distinguished by serological methods and are related more distantly to MmmSC, should be combined into a single subspecies, i.e. Mycoplasma mycoides subsp. capri, leaving M. mycoides subsp. mycoides (MmmSC) as the exclusive designation for the agent of contagious bovine pleuropneumonia. A taxonomic description of M. leachii sp. nov. and emended descriptions of M. mycoides subsp. mycoides and M. mycoides subsp. capri are presented. As a result of these emendments, the M. mycoides cluster will hereafter be composed of five taxa comprising three subclusters, which correspond to the M. mycoides subspecies, the M. capricolum subspecies and the novel species M. leachii.

The past ecology of Abies alba provides new perspectives on future responses of silver fir forests to global warming

Paleoecology can provide valuable insights into the ecology of species that complement observation and experiment-based assessments of climate impact dynamics. New paleoecological records (e.g., pollen, macrofossils) from the Italian Peninsula suggest a much wider climatic niche of the important European tree species Abies alba (silver fir) than observed in its present spatial range. To explore this discrepancy between current and past distribution of the species, we analyzed climatic data (temperature, precipitation, frost, humidity, sunshine) and vegetation-independent paleoclimatic reconstructions (e.g., lake levels, chironomids) and use global coupled carbon-cycle climate (NCAR CSM1.4) and dynamic vegetation (LandClim) modeling. The combined evidence suggests that during the mid-Holocene (6000 years ago), prior to humanization of vegetation, A. alba formed forests under conditions that exceeded the modern (1961-1990) upper temperature limit of the species by 5-7°C (July means). Annual precipitation during this natural period was comparable to today (>700-800 mm), with drier summers and wetter winters. In the meso-Mediterranean to sub-Mediterranean forests A. alba co-occurred with thermophilous taxa such as Quercus ilex, Q. pubescens, Olea europaea, Phillyrea, Arbutus, Cistus, Tilia, Ulmus, Acer, Hedera helix, Ilex aquifolium, Taxus, and Vitis. Results from the last interglacial (ca. 130 000-115 000 BP), when human impact was negligible, corroborate the Holocene evidence. Thermophilous Mediterranean A. alba stands became extinct during the last 5000 years when land-use pressure and specifically excessive anthropogenic fire and browsing disturbance increased. Our results imply that the ecology of this key European tree species is not yet well understood. On the basis of the reconstructed realized climatic niche of the species, we anticipate that the future geographic range of A. alba may not contract regardless of migration success, even if climate should become significantly warmer than today with summer temperatures increasing by up to 5-7°C, as long as precipitation does not fall below 700-800 mm/yr, and anthropogenic disturbance (e.g., fire, browsing) does not become excessive. Our finding contradicts recent studies that projected range contractions under global-warming scenarios, but did not factor how millennia of human impacts reduced the realized climatic niche of A. alba.

The new Southeast Asian goblin spider genus Aposphragisma (Araneae, Oonopidae): diversity and phylogeny

The new genus Aposphragisma (Araneae, Oonopidae, Oonopinae) comprising the new species A. baltenspergerae, A. borgulai, A. brunomanseri, A. confluens, A. dayak, A. dentatum, A. draconigenum, A. hausammannae, A. helvetiorum, A. kolleri, A. menzi, A. monoceros, A. nocturnum, A. retifer, A. rimba, A. salewskii, A. scimitar, A. sepilok and A. stannum is described. It is characterised by very hard bodied, strongly sclerotized species with completely armoured prosoma and strongly sclerotized ventral and dorsal abdominal scuta. Aposphragisma gen. nov. is placed within the Gamasomorpha-group sensu Saaristo (2001). Descriptions and illustrations are given for all new species. A phylogenetic analysis based on 40 characters using Prethopalpus fosuma, Gamasomorpha asterobothros, G. cataphracta, G. seximpressa, Xestaspis biflocci, X. kandy and X. paulina as outgroup-taxa and Cortestina thaleri (Oonopidae, Sulsulinae) as the root is presented and discussed. Furthermore it is shown that females of Aposphragisma gen. nov. possess complex internal genitalia. The members of the new genus are ground-dwelling litter inhabitants restricted to Southeast Asian lowland and montane forests, with more than 60% of the species only known from single localities. They are presumed to be negatively affected by the massive destruction of pristine forest habitats within their range. This work has been conducted within the framework of the Planetary Biodiversity Inventory (PBI) of Oonopidae (see http://research.amnh.org/oonopidae).

Silicoflagellates and ebridians from the New Jersey Transect DSDP Leg 93

Well-preserved and diverse silicoflagellate and ebridian populations are found in the lower and middle Eocene sediments of DSDP Site 605 and the upper Miocene sediments of DSDP Site 604. The ebridians outnumber the silicoflagellates in the siliceous interval of Site 605, but are less numerous at Site 604. The abundances of the various taxa are tabulated.

Distribution of deep-sea foraminifera in surface sediments east of New Zealand

Paleobathymetric assessments of fossil foraminiferal faunas play a significant role in the analysis of the paleogeographic, sedimentary, and tectonic histories of New Zealand's Neogene marine sedimentary basins. At depths >100 m, these assessments often have large uncertainties. This study, aimed at improving the precision of paleodepth assessments, documents the present-day distribution of deep-sea foraminifera (>63 µm) in 66 samples of seafloor sediment at 90-700 m water depth (outer shelf to mid-abyssal), east of New Zealand. One hundred and thirty-nine of the 465 recorded species of benthic foraminifera are new records for the New Zealand region. Characters of the foraminiferal faunas which appear to provide the most useful information for estimating paleobathymetry are, in decreasing order of reliability: relative abundance of common benthic species; benthic species associations; upper depth limits of key benthic species; and relative abundance of planktic foraminifera. R mode cluster analysis on the quantitative census data of the 58 most abundant species of benthic foraminifera produced six species associations within three higher level clusters: (1) calcareous species most abundant at mid-bathyal to outer shelf depths (<1000 m); (2) calcareous species most abundant at mid-bathyal and greater depths (>600 m); (3) agglutinated species mostly occurring at deep abyssal depths (>3000 m). A detrended correspondence analysis ordination plot exhibits a strong relationship between these species associations and bathymetry. This is manifest in the bathymetric ranges of the relative abundance peaks of many of the common benthic species (e.g., Abditodentrix pseudothalmanni 500-2800 m, Bolivina robusta 200-650 m, Bulimina marginata f. marginata 20-600 m, B. marginata f. aculeata 400-3000 m, Cassidulina norvangi 1000-4500 m, Epistominella exigua 1000-4700 m, and Trifarina angulosa 10-650 m), which should prove useful in paleobathymetric estimates. The upper depth limits of 28 benthic foraminiferal species (e.g., Fursenkoina complanata 200 m, Bulimina truncana 450 m, Melonis affinis 550 m, Eggerella bradyi 750 m, and Cassidulina norvangi 1000 m) have potential to improve the precision of paleobathymetric estimates based initially on the total faunal composition. The planktic percentage of foraminiferal tests increases from outer shelf to upper abyssal depths followed by a rapid decline within the foraminiferal lysocline (below c. 3600 m). A planktic percentage <50% is suggestive of shelf depths, and >50% is suggestive of bathyal or abyssal depths above the CCD. In the abyssal zone there is dramatic taphonomic loss of most agglutinated tests (except some textulariids) at burial depths of 0.1-0.2 m, which negates the potential usefulness of these taxa in paleobathymetric assessments.

Paleocene radiolarian distribution and biostratigraphy from offshore eastern New Zealand

A 100-m-thick Paleocene sequence of mainly pelagic sediments at ODP Site 1121, on the eastern flanks of the Campbell Plateau, contains few to common radiolarians of relatively low diversity in the lower 40 m (Early to early Late Paleocene) and abundant, diverse radiolarian assemblages in the upper 60 m (mid-Late Paleocene). The 150 taxa recorded from the entire Paleocene interval are thought to under-represent the actual species diversity by at least one half as many morphotypes have not been differentiated below the level of genus. Assemblages in the lower 40 m are similar to those described from onland New Zealand and DSDP Site 208 (northern Lord Howe Rise); they are correlated with South Pacific radiolarian zones RP4 and RP5. Assemblages in the upper 60 m differ from other known Late Paleocene assemblages in the great abundance of plagiacanthids and cycladophorids. Similarities are noted with later Cenozoic cool-water assemblages. This upper interval is correlated with South Pacific zone RP6, as revised herein, based on comparison with faunas from Site 208 and Marlborough, New Zealand. The interval is also correlated with the upper part of North Atlantic zone RP6 (RP6b-c) based on the presence of Aspis velutochlamydosaurus, Plectodiscus circularis and Pterocodon poculum. Other species, such as Buryella tetradica and Buryella pentadica, are valuable for local correlation but exhibit considerable diachroneity between the Pacific, Indian and Atlantic Oceans. An age model for the Paleocene interval at Site 1121, based on well-constrained nannofossil and radiolarian datums, indicates that the rate of compacted sediment accumulation doubles from 15 to 30 mm/ka at the RP5/RP6 zonal boundary. In large part this is due to a sudden and pronounced increase in accumulation rates for all siliceous fossils; radiolarians and larger diatoms increase from <100 to >10 000 specimens/cm2/ka. This apparent increase in biosiliceous productivity is age-equivalent to a mid-Paleocene cooling event (57-59 Ma) identified from global stable isotope records that is associated with the heaviest delta13C values for the entire Cenozoic.

Response of nannoplankton to major changes in sea-surface temperature at the South Chatham Rise, southeastern New Zealand

A high-resolution history of paleoceanographic changes in the subpolar waters of the southern margin of the Subtropical Convergence Zone during the last 130 kyr, is present in foraminiferal assemblages of DSDP Site 594. The foraminifera indicate that sea-surface temperatures during the Last Interglacial Climax were warmer than today, and that between substage 5d through to the end of isotope stage 2, temperatures were mostly cooler than Holocene temperatures. The paleotemperatures suggest that (1) the Subtropical Convergence was located over the site during substage 5e, later moving further north, then moving southwards to near the site during the Holocene, and (2) the Polar Front was positioned over the Site during glacial stages 6, 4, 2 and possibly parts of stage 3. Several major events are indicated by the nannofloral assemblages during these large changes in sea-surface temperature and associated reorganization of ocean circulation. First, the time-progressive trends between E. huxleyi and medium to large Gephyrocupsa are unique to this site, with E. huxleyi dominating over medium Gephyrocupsa during stages 5c-a, middle part of stage 4 and after the middle point of stage 3. This unusual trend may (at least partly) be caused by the shift of the Polar Front across the site. Second, upwelling flora (E. huxleyi and small placoliths) increase in abundance during stages 1, 3 and 5, suggesting that upwelling or disturbance of water stratification took place during the interglacials. Thirdly, there are no significant differences between the distribution patterns of the various morphotypes of medium to large Gephyrocupsu, and the combined value of all medium Gephyrocupsu increases in abundance during glacials (stages 2 and 4 and the end of stage 6), similar to the abundance trends in benthic foraminifera. Finally, subordinate nannofossil taxa also show distinctive climatic trends during the last glacial cycle: (1) Syrucosphaera spp. are present in increased abundance during warmer extremes in climate (substages 5e, 5a, and stage 1); (2) Coccolithus pelagicus and Culcidiscus leptoporus dominate the subordinate nannofossil taxa, and their relative proportions seem to provide a useful paleoceanographic index, with C. pelagicus dominating when the Polar Front Zone is over the site (stages 6, 4 and 2), whilst C. leptoporus is relatively more abundant when the STC is positioned over the site (stages 1 and 5e). Increased abundance of C. pelagicus also can indicate intensified coastal upwelling.

Coccolithophore taxa and PCA factor analysis of ODP Site 1233

We provide high-resolution sea surface temperature (SST) and paleoproductivity data focusing on Termination 1. We describe a new method for estimating SSTs based on multivariate statistical analyses performed on modern coccolithophore census data, and we present the first downcore reconstructions derived from coccolithophore assemblages at Ocean Drilling Project (ODP) Site 1233 located offshore Chile. We compare our coccolithophore SST record to alkenone-based SSTs as well as SST reconstructions based on dinoflagellates and radiolaria. All reconstructions generally show a remarkable concordance. As in the alkenone SST record, the Last Glacial Maximum (LGM, 19-23 kyr B.P.) is not clearly defined in our SST reconstruction. After the onset of deglaciation, three major warming steps are recorded: from 18.6 to 18 kyr B.P. (~2.6°C), from 15.7 to 15.3 kyr B.P. (~2.5°C), and from 13 to 11.4 kyr B.P. (~3.4°C). Consistent with the other records from Site 1233 and Antarctic ice core records, we observed a clear Holocene Climatic Optimum (HCO) from ~8-12 kyr B.P. Combining the SST reconstruction with coccolith absolute abundances and accumulation rates, we show that colder temperatures during the LGM are linked to higher coccolithophore productivity offshore Chile and warmer SSTs during the HCO to lower coccolithophore productivity, with indications of weak coastal upwelling. We interpret our data in terms of latitudinal displacements of the Southern Westerlies and the northern margin of the Antarctic Circumpolar Current system over the deglaciation and the Holocene.

Molecular fingerprinting and amplicon sequencing of the bacterial biofilm on settlement tiles deployed along natural pH gradients in Papua New Guinea

Bacterial biofilms provide cues for the settlement of marine invertebrates such as coral larvae, and are therefore important for the resilience and recovery of coral reefs. This study aimed to better understand how ocean acidification may affect the community composition and diversity of bacterial biofilms on surfaces under naturally reduced pH conditions. Settlement tiles were deployed at coral reefs in Papua New Guinea along pH gradients created by two CO2 seeps, and upper and lower tiles surfaces were sampled 5 and 13 months after deployment. Automated Ribosomal Intergenic Spacer Analysis were used to characterize more than 200 separate bacterial communities, complemented by amplicon sequencing of the bacterial 16S rRNA gene of 16 samples. The bacterial biofilm consisted predominantly of Alpha-, Gamma- and Deltaproteobacteria, as well as Cyanobacteria, Flavobacteriia and Cytophaga, whereas putative settlement-inducing taxa only accounted for a small fraction of the community. Bacterial biofilm composition was heterogeneous with approximately 25% shared operational taxonomic units between samples. Among the observed environmental parameters, pH only had a weak effect on community composition (R² ~ 1%) and did not affect community richness and evenness. In contrast, there were strong differences between upper and lower surfaces (contrasting in light exposure and grazing intensity). There also appeared to be a strong interaction between bacterial biofilm composition and the macroscopic components of the tile community. Our results suggest that on mature settlement surfaces in situ, pH does not have a strong impact on the composition of bacterial biofilms. Other abiotic and biotic factors such as light exposure and interactions with other organisms may be more important in shaping bacterial biofilms than changes in seawater pH.