The Pangenome of the Plant-Selected Rhizobium leguminosarum bv viciae Sub-popuations

Rhizobium leguminosarum bv viciae (Rlv) is a bacterium able to establish effective symbioses with four different legume genera: Pisum, Lens, Lathyrus and Vicia. Classic studies using trap plants have previously shown that, given a choice, different plants prefer specific genotypes of rhizobia, which are adapted to the host (1, 2). In previous work we have performed a Pool-Seq analysis bases on pooled DNA samples from Rlv nodule isolates obtained from Pisum sativum, Lens culinaris, Vicia fava and V. sativa plants, used as rhizobial traps. This experiment allowed us to test the host preference hypothesis: different plant hosts select specific sub-populations of rhizobia from the available population present in a given soil. We have observed that plant-selected sub-populations are different at the single nucleotide polymorphism (SNP) level. We have selected individual isolates from each sub-population (9 fava-bean isolates, 14 pea isolates 9 vetch isolates and 9 lentil isolates) and sequenced their genomes at draft level (ca. 30x, 90 contigs). Genomic analyses have been carried out using J-species and CMG-Biotools. All the isolates had similar genome size (7.5 Mb) and number of genes (7,300). The resulting Average Nucleotide Identity (ANIm) tree showed that Rhizobium leguminosarum bv viciae is a highly diverse group. Each plant-selected subpopulation showed a closed pangenome and core genomes of similar size (11,500 and 4,800 genes, respectively). The addition of all four sub-population results in a larger, closed pangenome of 19,040 genes and a core genome of similar size (4,392 genes). Each sub-population contains a characteristic set of genes but no universal, plant-specific genes were found. The core genome obtained from all four sub-populations is probably a representative core genome for Rhizobium leguminosarum, given that the reference genome (Rhizobium leguminosarum bv. viciae strain 3841) contains most of the core genome. We have also analyzed the symbiotic cluster (nod), and different nod cluster genotypes were found in each sub-population. Supported by MINECO (Consolider-Ingenio 2010, MICROGEN Project, CSD2009-00006).

(Table 1) Paleomagnetic of reoriented core pieces of IODP Hole 304-U1309D

Oceanic core complexes expose lower crustal and upper mantle rocks on the seafloor by tectonic unroofing in the footwalls of large-slip detachment faults. The common occurrence of these structures in slow and ultra-slow spread oceanic crust suggests that they accommodate a significant component of plate divergence. However, the subsurface geometry of detachment faults in oceanic core complexes remains unclear. Competing models involve either: (a) displacement on planar, low-angle faults with little tectonic rotation; or (b) progressive shallowing by rotation of initially steeply dipping faults as a result of flexural unloading (the "rolling-hinge" model). We address this debate using palaeomagnetic remanences as markers for tectonic rotation within a unique 1.4 km long footwall section of gabbroic rocks recovered by Integrated Ocean Drilling Program (IODP) sampling at Atlantis Massif oceanic core complex on the Mid-Atlantic Ridge (MAR). These rocks contain a complex record of multipolarity magnetizations that are unrelated to alteration and igneous stratigraphy in the sampled section and are inferred to result from progressive cooling of the footwall section over geomagnetic polarity chrons C1r.2r, C1r.1n (Jaramillo) and C1r.1r. For the first time we have independently reoriented drill-core samples of lower crustal gabbros, that were initially azimuthally unconstrained, to a true geographic reference frame by correlating structures in individual core pieces with those identified from oriented imagery of the borehole wall. This allows reorientation of the palaeomagnetic data, placing far more rigorous constraints on the tectonic history than those possible using only palaeomagnetic inclination data. Analysis of the reoriented high temperature reversed component of magnetization indicates a 46° ± 6° anticlockwise rotation of the footwall around a MAR-parallel horizontal axis trending 011° ± 6°. Reoriented lower temperature components of normal and reversed polarity suggest that much of this rotation occurred after the end of the Jaramillo chron (0.99 Ma). The data provide unequivocal confirmation of the key prediction of flexural, rolling-hinge models for oceanic core complexes, whereby oceanic detachment faults initiate at higher dips and rotate to their present day low-angle geometries as displacement increases.

Grain size analysis on core plugs of sediment core CRP-1 (Table 1, 2)

Twenty four core samples from CRP-1, seven from Quaternary strata (20-43.55 meters below sea floor or mbsf) and seventeen from early Miocene strata (43.55 to 147.69 mbsf), have been analysed for their grain-size distribution using standard sieve and Sedigraph techniques. The results are in good agreement with estimates of texture made as part of the visual core description for the 1 :20 core logs for CRP-1 (Cape Roberts Science Team, 1998). Interpretation of the analyses presented here takes into account the likely setting of the site in Quaternary times as it is today, with CRP-1 high on the landward flank of a well-defined submarine ridge rising several hundred metres above basins on either side. In contrast, seismic geometries for strata deposited in early Miocene times indicate a generally planar sea floor dipping gently seaward. Fossils from these strata indicate shallow water depths (< 100 m), indicating the possibility that waves and tidal currents may have influenced sea floor sediments. The sediments analysed here are considered in terms of 3 textural facies: diamict, mud (silt and clay) and sand. Most of the Quaternary section but only 30% of the early Miocene section is diamict, a poorly sorted mixture of sand and mud with scattered clasts, indicating little wave or current influence on its texture. Although not definitive, diamict textures and other features suggest that the sediment originated as basal glacial debris but has been subsequently modified by minor winnowing, consistent with the field interpretation of this facies as ice-proximal and distal glaciomarine sediment. Sediments deposited directly from glacier ice appear to be lacking. Mud facies sediments, which comprise only 10% of the Quaternary section but a third of the early Miocene section, were deposited below wave base and largely from suspension, and show features (described elsewhere in this volume) indicative of the influence of both glacial and sediment gravity flow processes. Sand facies sediments have a considerable proportion of mud, normally more than 20%, but a well-sorted fine-very fine sand fraction. In the context of the early Miocene coastal setting we interpret these sediments as shoreface sands close to wave base.

Investigation of Miocene foraminifera in sediment core CRP-1 from the Ross Sea, Antarctica

A faunal comprising 18 foraminiferal taxa wa recovered from a suite of 52 core samples from lower Miocene sandstone, claystone and diamictite in the CRP-1 drillhole, Cape Roberts, Antarctica. The fauna is characterised by low foraminiferal abundance and diversity, the absence of planktics, and typically, the presence of Cribroelphidium sp. and/or Melonis spp. These factors indicate deposition in an inner shelf or nearshore environment. Many of the foraminifers found in CRP-1 also occure in the upper Oligocene-Miocene sequences in CIROS-1 and DSDP-270, but the fauna provides no precise indication of age. Typical and distinctive species from CRP-1 are illustrated with SEM photomicrographs.

Glycerol dialkyl glycerol tetraethers (GDGT) abundance of sediment core GeoB15103-1

Marine microorganisms adapt to their habitat by structural modification of their membrane lipids. This concept is the basis of numerous molecular proxies used for paleoenvironmental reconstruction. Archaeal tetraether lipids from ubiquitous marine planktonic archaea are particularly abundant, well preserved in the sedimentary record and utilized in several molecular proxies. We here introduce the direct, extraction-free analysis of these compounds in intact sediment core sections using laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). LDI FTICR-MS can detect the target lipids in single sub-mm sized spots on sediment sections, equivalent to a sample mass in the nanogram range, and could thus pave the way for biomarker-based reconstruction of past environments and ecosystems at subannual to decadal resolution. We demonstrate that ratios of selected archaeal tetraethers acquired by LDI FTICR-MS are highly correlated with values obtained by conventional LC/MS protocols. The ratio of the major archaeal lipids, caldarchaeol and crenarchaeol, analyzed in a 6.2-cm intact section of Mediterranean sapropel S1 at 250-µm resolution (~4-year temporal resolution), provides an unprecedented view of the fine-scale patchiness of sedimentary biomarker distributions and the processes involved in proxy signal formation. Temporal variations of this lipid ratio indicate a strong influence of the 200-yr de Vries solar cycle on reconstructed sea surface temperatures with possible amplitudes of several degrees, and suggest signal amplification by a complex interplay of ecological and hydrological factors. Laser-based biomarker analysis of geological samples has the potential to revolutionize molecular stratigraphic studies of paleoenvironments.

Element abundances, loss on ignition, total analyzed abundances, CIA values, and Al-oxide/Ti-oxide ratios of sediment core CRP-2A (Table1)

The CRP-2/2A core, drilled in western McMurdo Sound in October and November 1998, penetrated 624 m of Quaternary. Pliocene, lower Miocene, and Oligocene glacigenic sediments. The palaeoclimatic record of CRP-2/2A is examined using major element analyses of bulk core samples of fine grained sediments (mudstones and siltstones) and the Chemical Index of Alteration (CIA) of Nesbitt & Young (1982). The CIA is calculated from the relative abundances of AI, K, Ca, and Na oxides, and its magnitude increases as the effects of chemical weathering increase. However, changes in sediment provenance can also affect the CIA, and provenance changes are recorded by shifts in the Al2O3/TiO2 ratios and the Nb contents of these CRP-2/2A mudstones. Relatively low CIA values (40-50) occur throughout the CRP-2/2A sequence, whereas the Al2O3/TiO2 ratio decreases upsection. The major provenance change is an abrupt onset of McMurdo Volcanic Group detritus at ~300 mbsf and is best characterized by a rapid increase in Nb content in the sediments. This provenance shift is not evident in the CIA record, suggesting that a contribution from the Ferrar Dolerite to the older sediments was replaced by an input of McMurdo Volcanic Group material in the younger sediments. If this is true, then the relatively uniform CIA values indicate relatively consistent palaeoweathering intensities throughout the Oligocene and early Miocene in the areas that supplied sediment to CRP-2/2A.

(Table 1) Lipid yields for samples across the Cretaceous/Tertiary boundary in DSDP Hole 86-577

Core samples of calcareous sediments taken from above and below the proposed Cretaceous/Tertiary boundary (Sample 577-12-5, 130 cm) were examined for geochemical evidence of the mass extinctions and faunal successions that marked this period. The lipid compositions of the six core samples examined were virtually identical and were characterized by a large component of unresolved naphthenic hydrocarbons and a homologous series of an/mo-alkanes, both presumably of bacterial origin. The results of this preliminary study suggest that the lipids of sediments deposited over a several million year period encompassing the Cretaceous-Tertiary extinctions have been almost completely recycled by bacterial metabolism, which occurred under oxic depositional and/or diagenetic conditions and which left a unique bacterial signature with only minor traces of the original sedimentary lipids.

Geochemistry of sediment samples from ODP Leg 135 holes

The results of inductively coupled argon plasma (ICAP) chemical analyses carried out on some 300 core samples from Ocean Drilling Program Sites 834, 835, 838, and 839 are presented. These sites were drilled during Leg 135 in the Lau Basin. The data are compared with total gamma (SGR) wireline logs at Sites 834 and 835. Pliocene (Piacenzian) nannofossil Zone CN12, which has been identified at Sites 834 and 835, is examined in detail using spectral analyses on core and wireline logs. The potassium and calcium concentrations from the core material were used to calculate an objective depth-to-geological time stretching function, which improved the stratigraphic correlation between sites. The integrated use of chemical analyses, wireline-log data and paleomagnetic results improved confidence in the correlations obtained. Although no significant sedimentation periodicities were obtained from the two sites, a common concentration of energy between 30 and 60 k.y. was recorded.