Publications

4479

Oil-rich sediments from the Gulf of Mexico were found to contain diverse alkane-degrading groups of archaea. The symbiotic, consortium-forming “ Candidatus Argoarchaeum” and “ Candidatus Syntrophoarchaeum” are likely responsible for the degradation of ethane and short-chain alkanes, with the help of sulfate-reducing bacteria. “ Ca. Methanoliparia” occurs as single cells associated with oil droplets. These archaea encode two phylogenetically different methyl-coenzyme M reductases that may allow this organism to thrive as a methanogen on a substrate of long-chain alkanes. Based on a library survey, we show that “ Ca. Methanoliparia ” is frequently detected in oil reservoirs and may be a key agent in the transformation of long-chain alkanes to methane. Our findings provide evidence for the important and diverse roles of archaea in alkane-rich marine habitats and support the notion of a significant functional versatility of the methyl coenzyme M reductase.

Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.

En Montecillo Texcoco, Estado de México se observaron plantas de margarita (<em>Dimorphotheca</em> <em>sinuata</em>) exhibiendo síntomas de filodia, virescencia y proliferación de ramas axilares putativos a los inducidos por fitoplasmas.  Por lo que el objetivo de esta investigación fue detectar el fitoplasma asociado a estos síntomas mediante PCR con los iniciadores P1/P7 y R16F2n/R2. Se detectó la presencia de fitoplasmas en tejido foliar sintomático. El producto de PCR de 1200 pb obtenido de la PCR  se secuenció y sometió a digestión con las enzimas de restricción MseI (Tru91), AluI, Kpn1 y HaIII, los patrones de restricción evidenciaron que el fitoplasma presente en <em>Dimorphotheca</em> <em>sinuata</em> es <em>Candidatus</em> phytoplasma asteris (16SrI). Las secuencias obtenidas fueron depositadas en la base de datos del NCBI y tuvieron una similitud del 99% con <em>Candidatus</em> phytoplasm asteris grupo 16Sr1-B de Irán (MH638316.1). Se realizó un análisis filogenético con el método de Neighbour-Joining, en el cual el aislamiento detectado en margarita, se agrupó con <em>Candidatus</em> phytoplasma asteris. De acuerdo con los síntomas observados en campo, análisis de patrones de restricción, secuenciación y filogenia, indican que la filodia en margarita está asociada a <em>Candidatus</em> phytoplasma asteris, relacionado filogenéticamente al grupo 16Sr1-B.

High levels of ‘Candidatus Phytoplasma pini’ have produced extensive forest mortality on Pinus halepensis Mill forests in eastern Spain. This has led to the widespread levels of forest mortality. We used archival Landsat imagery and shapes algorithm implemented in the Google Earth Engine to explore the potential of the LandTrendr algorithm and its outputs, together with field observations, to analyze and predict the health status in P. halepensis stands affected by ‘Candidatus Phytoplasma pini’ in Andalusia (south-eastern Spain). We found that the Landsat time series algorithm (LandTrendr) has captured both long- and short-duration trends and changes in spectral reflectance related to phytoplasma disturbance in the Aleppo pine forest stands investigated. The normalized burn ratio (NBR) trends were positively associated with environmental variables: Annual precipitation, mean temperature, soil depth, percent base saturation and aspect. Environmental variables were tested for their contributions to the mapping of changes in Aleppo pine cover in the study area, as an empirical modeling approach to disturbance mapping in forests of south-eastern Spain. The methodology outlined in this paper has produced valuable results that indicate new possibilities for the use in forest management of remote-sensing technologies based on spectral trajectories associated with pest-diseases defoliation. Given the likely increase in pest risks in the forests of southern Europe, accurate assessment and map of pest outbreaks on forests will become increasingly important, both for research and for practical applications in forest management.

ABSTRACTChain elongation is emerging as a bioprocess to produce valuable medium-chain fatty acids (MCFA; 6 to 8 carbons in length) from organic waste streams by harnessing the metabolism of anaerobic microbiomes. Although our understanding of chain elongation physiology is still evolving, the reverse β-oxidation pathway has been identified as a key metabolic function to elongate the intermediate products of fermentation to MCFA. Here, we describe two chain-elongating microorganisms that were enriched in an anaerobic microbiome transforming the residues from a lignocellulosic biorefining process to short- and medium-chain fatty acids. Based on a multi-omic analysis of this microbiome, we predict thatCandidatusWeimerbacter bifidus, gen. nov., sp. nov. used xylose to produce MCFA, whereasCandidatusPseudoramibacter fermentans, sp. nov., used glycerol and lactate as substrates for chain elongation. Both organisms are predicted to use an energy conserving hydrogenase to improve the overall bioenergetics of MCFA production.IMPORTANCEMicrobiomes are vital to human health, agriculture, environmental processes, and are receiving attention as biological catalysts for production of renewable industrial chemicals. Chain elongation by MCFA-producing microbiomes offer an opportunity to produce valuable chemicals from organic streams that otherwise would be considered waste. However, the physiology and energetics of chain elongation is only beginning to be studied, and we are analyzing MCFA production by self-assembled communities to complement the knowledge that has been acquired from pure culture studies. Through a multi-omic analysis of an MCFA-producing microbiome, we characterized metabolic functions of two chain elongating bacteria and predict previously unreported features of this process.

Abstract Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.

Abstract DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.

Monitoring the health of Huanglongbing-affected citrus trees by following changes in leaf Candidatus Liberibacter asiaticus (CLas) titer has an inherent element of imprecision because CLas titer varies considerably within the tree canopy and with calendar seasons. In addition, the destructive sampling method used to determine CLas titer entails a different set of leaves per sampling period adding to the inconsistency and inexactitude of the results. To overcome these ambiguities and to reduce the numerical variability between samples, we developed an experimental method that analyzes portions of the same treated leaves for up to four sampling periods. By assaying subsamples of adjacent locations of the same leaf, random variability was significantly reduced, and comparative analysis can be carried out with greater precision.