skip to main content


Title: Genome Sequences of Five Type Strain Members of the Archaeal Family Sulfolobaceae, Acidianus ambivalens, Acidianus infernus, Stygiolobus azoricus, Sulfuracidifex metallicus, and Sulfurisphaera ohwakuensis
ABSTRACT Presented are five genomes from the polyextremophilic (optimal temperature of >65°C and optimal pH of <3.5) archaeal family Sulfolobaceae , greatly expanding order-wide genomic diversity. Included are the only obligate anaerobic species, several facultative sulfur utilizers, two metal mobilizers, one facultative chemolithoautotroph with robust metabolic versatility, and some of the most thermophilic thermoacidophiles reported to date.  more » « less
Award ID(s):
1802939
NSF-PAR ID:
10162284
Author(s) / Creator(s):
; ; ;
Date Published:
Journal Name:
Microbiology Resource Announcements
Volume:
9
Issue:
11
ISSN:
2576-098X
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Globally, species are migrating in an attempt to track optimal isotherms as climate change increasingly warms existing habitats. Stony corals are severely threatened by anthropogenic warming, which has resulted in repeated mass bleaching and mortality events. Since corals are sessile as adults and with a relatively old age of sexual maturity, they are slow to latitudinally migrate, but corals may also migrate vertically to deeper, cooler reefs. Herein we describe vertical migration of the Mediterranean coral Oculina patagonica from less than 10 m depth to > 30 m. We suggest that this range shift is a response to rapidly warming sea surface temperatures on the Israeli Mediterranean coastline. In contrast to the vast latitudinal distance required to track temperature change, this species has migrated deeper where summer water temperatures are up to 2 °C cooler. Comparisons of physiology, morphology, trophic position, symbiont type, and photochemistry between deep and shallow conspecifics revealed only a few depth-specific differences. At this study site, shallow colonies typically inhabit low light environments (caves, crevices) and have a facultative relationship with photosymbionts. We suggest that this existing phenotype aided colonization of the mesophotic zone. This observation highlights the potential for other marine species to vertically migrate. 
    more » « less
  2. null (Ed.)
    Physiological preparations for migration generally reflect migratory strategy. Migrant birds fuel long-distance flight primarily with lipids, but carrying excess fuel is costly; thus, the amount of fat deposited prior to departure often reflects the anticipated flight duration or distance between refueling bouts. Seasonal pre-migratory deposition of fat is well documented in regular seasonal migrants, but is less described for more facultative species. We analyze fat deposits of free-living birds across several taxa of facultative migrants in the songbird subfamily Carduelinae, including house finches ( Haemorhous mexicanus ), American goldfinches ( Spinus tristis ), pine siskins ( Spinus pinus ) and four different North American ecotypes of red crossbills ( Loxia curvirostra ), to evaluate seasonal fat deposition during facultative migratory periods. Our data suggest that the extent of seasonal fat deposits corresponds with migratory tendency in these facultative taxa. Specifically, nomadic red crossbills with a seasonally predictable annual movement demonstrated relatively large seasonal fat deposits coincident with the migratory periods. In contrast, pine siskins, thought to be more variable in timing and initiation of nomadic movements, had smaller peaks in fat deposits during the migratory season, and the partial migrant American goldfinch and the resident house finch showed no peaks coincident with migratory periods. Within the red crossbills, those ecotypes that are closely associated with pine habitats showed larger peaks in fat deposits coincident with autumn migratory periods and had higher wing loading, whereas those ecotypes associated with spruces, Douglas-fir and hemlocks showed larger peaks coincident with spring migratory periods and lower wing loading. We conclude that population averages of fat deposits do reflect facultative migration strategies in these species, as well as the winter thermogenic challenges at the study locations. A difference in seasonal fattening and wing loading among red crossbill ecotypes is consistent with the possibility that they differ in their migratory biology, and we discuss these differences in light of crossbill reproductive schedules and phenologies of different conifer species. 
    more » « less
  3. Abstract Heritable symbionts are common in terrestrial arthropods and often provide beneficial services to hosts. Unlike obligate, nutritional symbionts that largely persist under strict host control within specialized host cells, heritable facultative symbionts exhibit large variation in within-host lifestyles and services rendered with many retaining the capacity to transition among roles. One enigmatic symbiont, Candidatus Fukatsuia symbiotica, frequently infects aphids with reported roles ranging from pathogen, defensive symbiont, mutualism exploiter and nutritional co-obligate symbiont. Here we used an in vitro culture-assisted protocol to sequence the genome of a facultative strain of Fukatsuia from pea aphids (Acyrthosiphon pisum). Phylogenetic and genomic comparisons indicate that Fukatsuia is an aerobic heterotroph, which together with Regiella insecticola and Hamiltonella defensa form a clade of heritable facultative symbionts within the Yersiniaceae (Enterobacteriales). These three heritable facultative symbionts largely share overlapping inventories of genes associated with housekeeping functions, metabolism, and nutrient acquisition, while varying in complements of mobile DNA. One unusual feature of Fukatsuia is its strong tendency to occur as a co-infection with H. defensa. However, the overall similarity of gene inventories among aphid heritable facultative symbionts suggest that metabolic complementarity is not the basis for co-infection, unless playing out on a H. defensa strain-specific basis. We also compared the pea aphid Fukatsuia with a strain from the aphid Cinara confinis (Lachninae) where it is reported to have transitioned to co-obligate status to support decaying Buchnera function. Overall the two genomes are very similar with no clear genomic signatures consistent with such a transition, which suggests co-obligate status in C. confinis was a recent event. 
    more » « less
  4. Abstract

    Groundwater‐dependent ecosystems are often defined by the presence of deeply rooted phreatophytic plants. When connected to groundwater, phreatophytes in arid regions decouple ecosystem net primary productivity from precipitation, underscoring a disproportionately high biodiversity and exchange of resources relative to surrounding areas. However, groundwater‐dependent ecosystems are widely threatened due to the effects of water diversions, groundwater abstraction, and higher frequencies of episodic drought and heat waves. The resilience of these ecosystems to shifting ecohydrological–climatological conditions will depend largely on the capacity of dominant, phreatophytic plants to cope with dramatic reductions in water availability and increases in atmospheric water demand. This paper disentangles the broad range of hydraulic traits expressed by phreatophytic vegetation to better understand their capacity to survive or even thrive under shifting ecohydrological conditions. We focus on three elements of plant water relations: (a) hydraulic architecture (including root area to leaf area ratios and rooting depth), (b) xylem structure and function, and (c) stomatal regulation. We place the expression of these traits across a continuum of phreatophytic habits from obligate to semi‐obligate to semi‐facultative to facultative. Although many species occupy multiple phreatophytic niches depending on access to groundwater, we anticipate that populations are largely locally adapted to a narrow range of ecohydrological conditions regardless of gene flow across ecohydrological gradients. Consequently, we hypothesize that reductions in available groundwater and increases in atmospheric water demand will result in either (a) stand replacement of obligate phreatophytic species with more facultative species as a function of widespread mortality in highly groundwater‐dependent populations or (b) directional selection in semi‐obligate and semi‐facultative phreatophytes towards the expression of traits associated with highly facultative phreatophytes in the absence of species replacement. Anticipated shifts in the expression of hydraulic traits may have profound impacts on water cycling processes, species assemblages, and habitat structure of groundwater‐dependent woodlands and riparian forests.

     
    more » « less
  5. Buan, Nicole R. (Ed.)
    ABSTRACT Sideroxydans lithotrophicus ES-1 grows autotrophically either by Fe(II) oxidation or by thiosulfate oxidation, in contrast to most other isolates of neutrophilic Fe(II)-oxidizing bacteria (FeOB). This provides a unique opportunity to explore the physiology of a facultative FeOB and constrain the genes specific to Fe(II) oxidation. We compared the growth of S. lithotrophicus ES-1 on Fe(II), thiosulfate, and both substrates together. While initial growth rates were similar, thiosulfate-grown cultures had higher yield with or without Fe(II) present, which may give ES-1 an advantage over obligate FeOB. To investigate the Fe(II) and S oxidation pathways, we conducted transcriptomics experiments, validated with reverse transcription-quantitative PCR (RT-qPCR). We explored the long-term gene expression response at different growth phases (over days to a week) and expression changes during a short-term switch from thiosulfate to Fe(II) (90 min). The dsr and sox sulfur oxidation genes were upregulated in thiosulfate cultures. The Fe(II) oxidase gene cyc2 was among the top expressed genes during both Fe(II) and thiosulfate oxidation, and addition of Fe(II) to thiosulfate-grown cells caused an increase in cyc2 expression. These results support the role of Cyc2 as the Fe(II) oxidase and suggest that ES-1 maintains readiness to oxidize Fe(II), even in the absence of Fe(II). We used gene expression profiles to further constrain the ES-1 Fe(II) oxidation pathway. Notably, among the most highly upregulated genes during Fe(II) oxidation were genes for alternative complex III, reverse electron transport, and carbon fixation. This implies a direct connection between Fe(II) oxidation and carbon fixation, suggesting that CO 2 is an important electron sink for Fe(II) oxidation. IMPORTANCE Neutrophilic FeOB are increasingly observed in various environments, but knowledge of their ecophysiology and Fe(II) oxidation mechanisms is still relatively limited. Sideroxydans isolates are widely observed in aquifers, wetlands, and sediments, and genome analysis suggests metabolic flexibility contributes to their success. The type strain ES-1 is unusual among neutrophilic FeOB isolates, as it can grow on either Fe(II) or a non-Fe(II) substrate, thiosulfate. Almost all our knowledge of neutrophilic Fe(II) oxidation pathways comes from genome analyses, with some work on metatranscriptomes. This study used culture-based experiments to test the genes specific to Fe(II) oxidation in a facultative FeOB and refine our model of the Fe(II) oxidation pathway. We gained insight into how facultative FeOB like ES-1 connect Fe, S, and C biogeochemical cycling in the environment and suggest a multigene indicator would improve understanding of Fe(II) oxidation activity in environments with facultative FeOB. 
    more » « less