No abstract

Circadian rhythms are important biological signals that have been found in almost all major groups of life from bacteria to man, yet it remains unclear if any members of the second major prokaryotic domain of life, the Archaea, also possess a biological clock. As an initial investigation of this question, we examined the regulation of four cyanobacterial-like circadian gene homologs present in the genome of the haloarchaeon Haloferax volcanii. These genes, designated cirA, cirB, cirC, and cirD, display similarity to the KaiC-family of cyanobacterial clock proteins, which act to regulate rhythmic gene expression and to control the timing of cell division. Quantitative RT-PCR analysis was used to examine the expression of each of the four cir genes in response to 12 h light/12 h dark cycles (LD 12:12) in H. volcanii during balanced growth. Our data reveal that there is an approximately two to sixteen-fold increase in cir gene expression when cells are shifted from light to constant darkness, and this pattern of gene expression oscillates with the light conditions in a rhythmic manner. Targeted single- and double-gene knockouts in the H. volcanii cir genes result in disruption of light-dependent, rhythmic gene expression, although it does not lead to any significant effect on growth under these conditions. Restoration of light-dependent, rhythmic gene expression was demonstrated by introducing, in trans, a wild-type copy of individual cir genes into knockout strains. These results are noteworthy as this is the first attempt to characterize the transcriptional expression and regulation of the ubiquitous kaiC homologs found among archaeal genomes.

Sorting the suffixes of a string into lexicographical order is a fundamental task in a number of contexts, most notably lossless compression (Burrows-Wheeler transformation) and text indexing (suffix arrays). Most approaches to suffix sorting produce a sorted array of suffixes directly, continually moving suffixes into their final place in the array until the ordering is complete. In this article, we describe a novel and resource-efficient (time and memory) approach to suffix sorting, which works in a complementary way-by assigning each suffix its rank in the final ordering, before converting to a sorted array, if necessary, once all suffixes are ranked. We layer several powerful extensions on this basic idea and show experimentally that our approach is superior to other leading algorithms in a variety of real-world contexts.

Diatoms contribute up to 40% of marine primary production 1 and have silicified cell walls that ballast substantial vertical flux of particulate organic matter out of the surface into the deep ocean 2 . In high-nutrient, low-chlorophyll regions of the open ocean and along some coastal upwelling margins, iron (Fe) availability limits diatom production [3][4][5] and may contribute to the decoupling of primary productivity and export efficiency in these waters [6][7][8] . Fe-limited waters are biogeochemically distinct, characterized by enhanced drawdown of silicic acid relative to nitrate by Fe-limited diatoms, which leads to high cellular silicon (Si):nitrogen (N) and Si:carbon (C) 9,10 . These regions can also exhibit elevated diatom carbon export efficiency 6-8 and markedly high burial of biogenic silica (bSiO 2 ) relative to organic carbon in underlying sediments 11 . These 'hot spots' of silica burial contribute to widespread limitation of diatom silica production rates in the surface ocean, linking the Fe, Si and C cycles, and may impose a global constraint on the drawdown of atmospheric CO 2 and export production [12][13][14] . Together, these observations underscore the importance of elucidating the underlying chemical, physical and biological interactions that dictate the fate of diatom organic matter and associated elements in the ocean.Viral infection of microbes is a major conduit for elemental cycling in the ocean, transforming the biogeochemical flux of nutrients and carbon, and toggling the balance between export and remineralization processes 15,16 . By fuelling the microbial loop with dissolved organic matter released during host lysis, viruses circumvent the transfer of particulate organic matter to depth or higher trophic levels through the 'viral shunt' 17 . We recently reported accelerated virus-mediated mortality in Si-limited diatoms, demonstrating a role for nutrient availability in facilitating the viral shunt 18 . However viral infection can also 'shuttle' organic matter out of the surface ocean by stimulating processes that facilitate export such as particle aggregation 19,20 and spore formation 21 , highlighting the dynamic, biogeochemical consequences of host-virus interactions. Here we explored diatom host-virus dynamics in Fe-limited regimes of the northeast Pacific Ocean.

Transitions in phytoplankton community composition are typically attributed to ecological succession even in physically dynamic upwelling systems like the California Current Ecosystem (CCE). An expected succession from a high‐chlorophyll (~ 10 μg L−1) diatom‐dominated assemblage to a low‐chlorophyll (< 1.0 μg L−1) non‐diatom dominated assemblage was observed during a 2013 summer upwelling event in the CCE. Using an interdisciplinary field‐based space‐for‐time approach leveraging both biogeochemical rate measurements and metatranscriptomics, we suggest that this successional pattern was driven primarily by physical processes. An annually recurring mesoscale eddy‐like feature transported significant quantities of high‐phytoplankton‐biomass coastal water offshore. Chlorophyll was diluted during transport, but diatom contributions to phytoplankton biomass and activity (49–62% observed) did not decline to the extent predicted by dilution (18–24% predicted). Under the space‐for‐time assumption, these trends infer diatom biomass and activity and were stimulated during transport. This is hypothesized to result from decreased contact rates with mortality agents (e.g., viruses) and release from nutrient limitation (confirmed by rate data nearshore), as predicted by the Disturbance‐Recovery hypothesis of phytoplankton bloom formation. Thus, the end point taxonomic composition and activity of the phytoplankton assemblage being transported by the eddy‐like feature were driven by physical processes (mixing) affecting physiological (release from nutrient limitation, increased growth) and ecological (reduced mortality) factors that favored the persistence of the nearshore diatoms during transit. The observed connection between high‐diatom‐biomass coastal waters and non‐diatom‐dominated offshore waters supports the proposed mechanisms for this recurring eddy‐like feature moving seed populations of coastal phytoplankton offshore and thereby sustaining their activity.