Use of 16S rRNA Gene Based Clone Libraries to Assess Microbial Communities Potentially Involved in Anaerobic Methane Oxidation in a Mediterranean Cold Seep

This study provides data on the diversities of bacterial and archaeal communities in an active methane seep at the Kazan mud volcano in the deep Eastern Mediterranean sea. Layers of varying depths in the Kazan sediments were investigated in terms of (1) chemical parameters and (2) DNA-based microbial population structures. The latter was accomplished by analyzing the sequences of directly amplified 16S rRNA genes, resulting in the phylogenetic analysis of the prokaryotic communities. Sequences of organisms potentially associated with processes such as anaerobic methane oxidation and sulfate reduction were thus identified. Overall, the sediment layers revealed the presence of sequences of quite diverse bacterial and archaeal communities, which varied considerably with depth. Dominant types revealed in these communities are known as key organisms involved in the following processes: (1) anaerobic methane oxidation and sulfate reduction, (2) sulfide oxidation, and (3) a range of (aerobic) heterotrophic processes. In the communities in the lowest sediment layer sampled (22–34 cm), sulfate-reducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic organisms abounded in the top sediment layer (0–6 cm). Communities in the middle layer (6–22 cm) contained organisms that could be linked to either of the aforementioned processes. We discuss how these phylogeny (sequence)-based findings can support the ongoing molecular work aimed at unraveling both the functioning and the functional diversities of the communities under study

Development of global temperature and pH calibrations based on bacterial 3-hydroxy fatty acids in soils

Gram-negative bacteria produce specific membrane lipids, i.e. 3-hydroxy fatty acids with 10 to 18 C atoms. They have been recently proposed as temperature and pH proxies in terrestrial settings. Nevertheless, the existing correlations between pH or temperature and indices derived from 3-OH FA distribution are based on a small soil dataset (ca. 70 samples) and only applicable regionally. The aim of this study was to investigate the applicability of 3-OH FAs as mean annual air temperature (MAAT) and pH proxies at the global level. This was achieved using an extended soil dataset of 168 topsoils distributed worldwide, covering a wide range of temperatures (5 to 30 ∘C) and pH (3 to 8). The response of 3-OH FAs to temperature and pH was compared to that of established branched glycerol dialkyl glycerol tetraether (GDGT)-based proxies (MBT'5Me/CBT). Strong linear relationships between 3-OH-FA-derived indices (RAN15, RAN17 and RIAN) and MAAT or pH could only be obtained locally for some of the individual transects. This suggests that these indices cannot be used as palaeoproxies at the global scale using simple linear regression models, in contrast with the MBT'5Me and CBT. However, strong global correlations between 3-OH FA relative abundances and MAAT or pH were shown by using other algorithms (multiple linear regression, k-NN and random forest models). The applicability of the three aforementioned models for palaeotemperature reconstruction was tested and compared with the MAAT record from a Chinese speleothem. The calibration based on the random forest model appeared to be the most robust. It generally showed similar trends with previously available records and highlighted known climatic events poorly visible when using local 3-OH FA calibrations. Altogether, these results demonstrate the potential of 3-OH FAs as palaeoproxies in terrestrial settings

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults

FROG: A global machine-learning temperature calibration for branched GDGTs in soils and peats

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are a family of bacterial lipids which have emerged over time as robust temperature and pH paleoproxies in continental settings. Nevertheless, it was previously shown that other parameters than temperature and pH, such as soil moisture, thermal regime or vegetation can also influence the relative distribution of brGDGTs in soils and peats. This can explain a large part of the residual scatter in the global brGDGT calibrations with mean annual air temperature (MAAT) and pH in these settings. Despite improvements in brGDGT analytical methods and development of refined models, the root-mean-square error (RMSE) associated with global calibrations between brGDGT distribution and MAAT in soils and peats remains high (∼5 °C). The aim of the present study was to develop a new global terrestrial brGDGT temperature calibration from a worldwide extended dataset (i.e. 775 soil and peat samples, i.e. 112 samples added to the previously available global calibration) using a machine learning algorithm. Statistical analyses highlighted five clusters with different effects of potential confounding factors in addition to MAAT on the relative abundances of brGDGTs. The results also revealed the limitations of using a single index and a simple linear regression model to capture the response of brGDGTs to temperature changes. A new improved calibration based on a random forest algorithm was thus proposed, the so-called random Forest Regression for PaleOMAAT using brGDGTs (FROG). This multi-factorial and non-parametric model allows to overcome the use of a single index, and to be more representative of the environmental complexity by taking into account the non-linear relationships between MAAT and the relative abundances of the individual brGDGTs. The FROG model represents a refined brGDGT temperature calibration (R2 = 0.8; RMSE = 4.01 °C) for soils and peats, more robust and accurate than previous global soil calibrations while being proposed on an extended dataset. This novel improved calibration was further applied and validated on two paleo archives covering the last 110 kyr and the Pliocene, respectively

Scientific drilling of Lake Chalco, Basin of Mexico (MexiDrill)

The primary scientific objective of MexiDrill, the Basin of Mexico Drilling Program, is development of a continuous, high-resolution ∼400 kyr lacustrine record of tropical North American environmental change. The field location, in the densely populated, water-stressed Mexico City region gives this record particular societal relevance. A detailed paleoclimate reconstruction from central Mexico will enhance our understanding of long-term natural climate variability in the North American tropics and its relationship with changes at higher latitudes. The site lies at the northern margin of the Intertropical Convergence Zone (ITCZ), where modern precipitation amounts are influenced by sea surface temperatures in the Pacific and Atlantic basins. During the Last Glacial Maximum (LGM), more winter precipitation at the site is hypothesized to have been a consequence of a southward displacement of the mid-latitude westerlies. It thus represents a key spatial node for understanding large-scale hydrological variability of tropical and subtropical North America and is at an altitude (2240 m a.s.l.), typical of much of western North America. In addition, its sediments contain a rich record of pre-Holocene volcanic history; knowledge of the magnitude and frequency relationships of the area's explosive volcanic eruptions will improve capacity for risk assessment of future activity. Explosive eruption deposits will also be used to provide the backbone of a robust chronology necessary for full exploitation of the paleoclimate record. Here we report initial results from, and outreach activities of, the 2016 coring campaign.</jats:p

Scientific drilling of Lake Chalco, Basin of Mexico (MexiDrill)

The primary scientific objective of MexiDrill, the Basin of Mexico Drilling Program, is development of a continuous, high-resolution ∼400 kyr lacustrine record of tropical North American environmental change. The field location, in the densely populated, water-stressed Mexico City region gives this record particular societal relevance. A detailed paleoclimate reconstruction from central Mexico will enhance our understanding of long-term natural climate variability in the North American tropics and its relationship with changes at higher latitudes. The site lies at the northern margin of the Intertropical Convergence Zone (ITCZ), where modern precipitation amounts are influenced by sea surface temperatures in the Pacific and Atlantic basins. During the Last Glacial Maximum (LGM), more winter precipitation at the site is hypothesized to have been a consequence of a southward displacement of the mid-latitude westerlies. It thus represents a key spatial node for understanding large-scale hydrological variability of tropical and subtropical North America and is at an altitude (2240 m a.s.l.), typical of much of western North America. In addition, its sediments contain a rich record of pre-Holocene volcanic history; knowledge of the magnitude and frequency relationships of the area's explosive volcanic eruptions will improve capacity for risk assessment of future activity. Explosive eruption deposits will also be used to provide the backbone of a robust chronology necessary for full exploitation of the paleoclimate record. Here we report initial results from, and outreach activities of, the 2016 coring campaign