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  • 1. Alonso-Saéz, Laura
    et al.
    Waller, Allison S
    Mende, Daniel R
    Bakker, Kevin
    Farnelid, Hanna
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Yager, Patricia L
    Lovejoy, Connie
    Tremblay, Jean-Eric
    Potvin, Marianne
    Heinrich, Friederike
    Estrada, Marta
    Riemann, Lasse
    Marine Biological Section, University of Copenhagen, 3000 Helsingør, Denmark .
    Bork, Peer
    Pedros-Alio, Carlos
    Bertilsson, Stefan
    Role for urea in nitrification by polar marine Archaea2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 44, p. 17989-17994Article in journal (Refereed)
    Abstract [en]

    Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.

  • 2.
    Bentzon-Tilia, Mikkel
    et al.
    Univ Copenhagen.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Jürgens, Klaus
    Leibniz Inst Balt Sea Res IOW, Germany.
    Riemann, Lasse
    Univ Copenhagen.
    Cultivation and isolation of N2-fixing bacteria from suboxic waters in the Baltic Sea2014In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 88, no 2, p. 358-371Article in journal (Refereed)
    Abstract [en]

    Nitrogenase genes (nifH) from heterotrophic dinitrogen (N-2)-fixing bacteria appear ubiquitous in marine bacterioplankton, but the significance of these bacteria for N cycling is unknown. Quantitative data on the N-2-fixation potential of marine and estuarine heterotrophs are scarce, and the shortage of cultivated specimens currently precludes ecophysiological characterization of these bacteria. Through the cultivation of diazotrophs from suboxic (1.79molO(2)L(-1)) Baltic Sea water in an artificial seawater medium devoid of combined N, we report the cultivability of a considerable fraction of the diazotrophic community in the Gotland Deep. Two nifH clades were present both in situ and in enrichment cultures showing gene abundances of up to 4.6x10(5) and 5.8x10(5)nifH gene copies L-1 within two vertical profiles in the Baltic Sea. The distributions of the two clades suggested a relationship with the O-2 concentrations in the water column as abundances increased in the suboxic and anoxic waters. It was possible to cultivate and isolate representatives from one of these prevalent clades, and preliminary analysis of their ecophysiology demonstrated growth optima at 0.5-15molO(2)L(-1) and 186-194molO(2)L(-1) in the absence of combined N.

  • 3.
    Bertos-Fortis, Mireia
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Casini, Michele
    Swedish University of Agricultural Sciences.
    Andersson, Agneta
    Umeå University.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors2016In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, article id 625Article in journal (Refereed)
    Abstract [en]

    Future climate scenarios in the Baltic Sea project an increase of cyanobacterial bloom frequency and duration, attributed to eutrophication and climate change. Some cyanobacteria can be toxic and their impact on ecosystem services is relevant for a sustainable sea. Yet, there is limited understanding of the mechanisms regulating cyanobacterial diversity and biogeography. Here we unravel successional patterns and changes in cyanobacterial community structure using a 2-year monthly time series during the productive season in a 100 km coastal-offshore transect using microscopy and high-throughput sequencing of 16S rRNA gene fragments. A total of 565 cyanobacterial OTUs were found, of which 231 where filamentous/colonial and 334 picocyanobacterial. Spatial differences in community structure between coastal and offshore waters were minor. An "epidemic population structure" (dominance of a single cluster) was found for Aphanizomenon/Dolichospermum within the filamentous/colonial cyanobacterial community. In summer, this cluster simultaneously occurred with opportunistic clusters/OTUs, e.g., Nodulana spumigena and Pseudanabaena. Picocyanobacteria, Synechococcus/Cyanobium, formed a consistent but highly diverse group. Overall, the potential drivers structuring summer cyanobacterial communities were temperature and salinity. However, the different responses to environmental factors among and within genera suggest high niche specificity for individual OTUs. The recruitment and occurrence of potentially toxic filamentous/colonial clusters was likely related to disturbance such as mixing events and short-term shifts in salinity, and not solely dependent on increasing temperature and nitrogen-limiting conditions. Nutrients did not explain further the changes in cyanobacterial community composition. Novel occurrence patterns were identified as a strong seasonal succession revealing a tight coupling between the emergence of opportunistic picocyanobacteria and the bloom of filamentous/colonial clusters. These findings highlight that if environmental conditions can partially explain the presence of opportunistic picocyanobacteria, microbial and trophic interactions with filamentous/colonial cyanobacteria should also be considered as potential shaping factors for single-celled communities. Regional climate change scenarios in the Baltic Sea predict environmental shifts leading to higher temperature and lower salinity; conditions identified here as favorable for opportunistic filamentous/colonial cyanobacteria. Altogether, the diversity and complexity of cyanobacterial communities reported here is far greater than previously known, emphasizing the importance of microbial interactions between filamentous and picocyanobacteria in the context of environmental disturbances.

  • 4.
    Cornejo-Castillo, Francisco M.
    et al.
    Univ Calif Santa Cruz, USA;CSIC, Spain.
    del Carmen Munoz-Marin, Maria
    Univ Calif Santa Cruz, USA;Univ Cordoba, Spain.
    Turk-Kubo, Kendra A.
    Univ Calif Santa Cruz, USA.
    Royo-Llonch, Marta
    CSIC, Spain.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Calif Santa Cruz, USA.
    Acinas, Silvia G.
    CSIC, Spain.
    Zehr, Jonathan P.
    Univ Calif Santa Cruz, USA.
    UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N2-fixing cyanobacterium Candidatus Atelocyanobacterium thalassa2019In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, no 1, p. 111-124Article in journal (Refereed)
    Abstract [en]

    The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is one of the most abundant and widespread nitrogen (N-2)-fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN-A1, UCYN-A2, UCYN-A3 and UCYN-A4. However, very little is known about UCYN-A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD-FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN-A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN-A3 sublineage. We designed new CARD-FISH probes that allowed us to distinguish and observe UCYN-A2 in a coastal location (SIO Pier; San Diego) and UCYN-A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN-A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN-A3 symbiosis in open ocean waters suggesting that the different UCYN-A sublineages are distributed along different size fractions of the plankton defined by the cell-size ranges of their prymnesiophyte hosts.

  • 5.
    del Carmen Munoz-Marin, Maria
    et al.
    Univ Calif Santa Cruz, USA;Univ Cordoba, Spain.
    Shilova, Irina N.
    Univ Calif Santa Cruz, USA;Second Genome Inc, USA.
    Shi, Tuo
    Univ Calif Santa Cruz, USA;Xiamen Univ, Peoples Republic of China.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Calif Santa Cruz, USA.
    Maria Cabello, Ana
    Univ Calif Santa Cruz, USA.
    Zehr, Jonathan P.
    Univ Calif Santa Cruz, USA.
    The Transcriptional Cycle Is Suited to Daytime N2 Fixation in the Unicellular Cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A)2019In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 10, no 1, p. 1-17, article id e02495-18Article in journal (Refereed)
    Abstract [en]

    Symbiosis between a marine alga and a N-2-fixing cyanobacterium (Cyanobacterium UCYN-A) is geographically widespread in the oceans and is important in the marine N cycle. UCYN-A is uncultivated and is an unusual unicellular cyanobacterium because it lacks many metabolic functions, including oxygenic photosynthesis and carbon fixation, which are typical in cyanobacteria. It is now presumed to be an obligate symbiont of haptophytes closely related to Braarudosphaera bigelowii. N-2-fixing cyanobacteria use different strategies to avoid inhibition of N-2 fixation by the oxygen evolved in photosynthesis. Most unicellular cyanobacteria temporally separate the two incompatible activities by fixing N-2 only at night, but, surprisingly, UCYN-A appears to fix N-2 during the day. The goal of this study was to determine how the unicellular UCYN-A strain coordinates N-2 fixation and general metabolism compared to other marine cyanobacteria. We found that UCYN-A has distinct daily cycles of many genes despite the fact that it lacks two of the three circadian clock genes found in most cyanobacteria. We also found that the transcription patterns in UCYN-A are more similar to those in marine cyanobacteria that are capable of aerobic N-2 fixation in the light, such as Trichodesmium and heterocyst-forming cyanobacteria, than to those in Crocosphaera or Cyanothece species, which are more closely related to unicellular marine cyanobacteria evolutionarily. Our findings suggest that the symbiotic interaction has resulted in a shift of transcriptional regulation to coordinate UCYN-A metabolism with that of the phototrophic eukaryotic host, thus allowing efficient coupling of N-2 fixation (by the cyanobacterium) to the energy obtained from photosynthesis (by the eukaryotic unicellular alga) in the light. IMPORTANCE The symbiotic N-2-fixing cyanobacterium UCYN-A, which is closely related to Braarudosphaera bigelowii, and its eukaryotic algal host have been shown to be globally distributed and important in open-ocean N-2 fixation. These unique cyanobacteria have reduced metabolic capabilities, even lacking genes for oxygenic photosynthesis and carbon fixation. Cyanobacteria generally use energy from photosynthesis for nitrogen fixation but require mechanisms for avoiding inactivation of the oxygen-sensitive nitrogenase enzyme by ambient oxygen (O-2) or the O-2 evolved through photosynthesis. This study showed that symbiosis between the N-2-fixing cyanobacterium UCYN-A and its eukaryotic algal host has led to adaptation of its daily gene expression pattern in order to enable daytime aerobic N-2 fixation, which is likely more energetically efficient than fixing N-2 at night, as found in other unicellular marine cyanobacteria.

  • 6.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Distribution and activity of nitrogen-fixing bacteria in marine and estuarine waters2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In aquatic environments the availability of nitrogen (N) generally limits primary production. N2-fixing prokaryotes (diazotrophs) can convert N2 gas into ammonium and provide significant input of N into the oceans. Cyanobacteria are thought to be the main N2-fixers but diazotrophs also include a wide range of heterotrophic bacteria. However, their activity and regulation in the water column is largely unknown.

    In this thesis the distribution, diversity, abundance, and activity of marine and estuarine heterotrophic diazotrophs was investigated. With molecular methods targeting the nifH gene, encoding the nitrogenase enzyme for N2 fixation, it was shown that diverse nifH genes affiliating with heterotrophic bacteria were ubiquitous in surface waters from ten marine locations world-wide and the estuarine Baltic Sea. Through enrichment cultures of Baltic Sea surface water in anaerobic N-free medium, heterotrophic N2 fixation was induced showing that there was a functional N2-fixing community present and isolates of heterotrophic diazotrophs were obtained. In Sargasso Sea surface waters, transcripts of nifH related to heterotrophic bacteria were detected indicating heterotrophic N2-fixing activity.

    Nitrogenase expression is thought to be highly regulated by the availability of inorganic N and the presence of oxygen. Low oxygen zones within the water column can be found in association with plankton. The presence of diazotrophs as symbionts of heterotrophic dinoflagellates was investigated and nifH genes related to heterotrophic diazotrophs rather than the cyanobacterial symbionts were found, suggesting that a symbiotic co-existence prevailed. Oxic-anoxic interfaces could also be potential sites for heterotrophic N2 fixation. The Baltic Sea contains large areas of anoxic bottom water. At the chemocline and in anoxic deep water heterotrophic diazotrophs were diverse, abundant and active. These findings extend the currently known regime of N2 fixation to also include ammonium-rich anaerobic waters.

    The results of this thesis suggest that heterotrophic diazotrophs are diverse and widely distributed in marine and estuarine waters and that they can also be active. However, limits in the knowledge on their physiology and factors which regulate their N2 fixation activity currently prevent an evaluation of their importance in the global marine N budget.

  • 7.
    Farnelid, Hanna
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Andersson, Anders F.
    Bertilsson, Stefan
    Al-Soud, Waleed Abu
    Hansen, Lars H
    Sørensen, Søren
    Steward, Grieg F
    Hagström, Åke
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Riemann, Lasse
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
    Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 4, p. e19223-Article in journal (Refereed)
    Abstract [en]

    Cyanobacteria are thought to be the main N(2)-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N(2) fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.

  • 8.
    Farnelid, Hanna
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bentzon-Tilia, Mikkel
    Andersson, Anders F.
    Bertilsson, Stefan
    Jost, Guenter
    Labrenz, Matthias
    Juergens, Klaus
    Riemann, Lasse
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Active nitrogen-fixing heterotrophic bacteria at and below the chemocline of the central Baltic Sea2013In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, no 7, p. 1413-1423Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea receives large nitrogen inputs by diazotrophic (N-2-fixing) heterocystous cyanobacteria but the significance of heterotrophic N-2 fixation has not been studied. Here, the diversity, abundance and transcription of the nifH fragment of the nitrogenase enzyme in two basins of the Baltic Sea proper was examined. N-2 fixation was measured at the surface (5 m) and in anoxic water (200 m). Vertical sampling profiles of >10 and <10 mu m size fractions were collected in 2007, 2008 and 2011 at the Gotland Deep and in 2011 in the Bornholm Basin. Both of these stations are characterized by permanently anoxic bottom water. The 454-pyrosequencing nifH analysis revealed a diverse assemblage of nifH genes related to alpha-, beta- and gammaproteobacteria (nifH cluster I) and anaerobic bacteria (nifH cluster III) at and below the chemocline. Abundances of genes and transcripts of seven diazotrophic phylotypes were investigated using quantitative polymerase chain reaction revealing abundances of heterotrophic nifH phylotypes of up to 2.1 x 10(7) nifH copies l(-1). Abundant nifH transcripts (up to 3.2 x 10(4) transcripts l(-1)) within nifH cluster III and co-occurring N-2 fixation (0.44 +/- 0.26 nmol l(-1) day(-1)) in deep water suggests that heterotrophic diazotrophs are fixing N2 in anoxic ammonium-rich waters. Our results reveal that N-2 fixation in the Baltic Sea is not limited to illuminated N-deplete surface waters and suggest that N-2 fixation could also be of importance in other suboxic regions of the world's oceans.

  • 9.
    Farnelid, Hanna
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Harder, Jens
    Max Planck Inst Marine Microbiol, Dept Microbiol, Bremen, Germany.
    Bentzon-Tilia, Mikkel
    Univ Copenhagen, Denmark.
    Riemann, Lasse
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Copenhagen, Denmark.
    Isolation of heterotrophic diazotrophic bacteria from estuarine surface waters2014In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 16, no 10, p. 3072-3082Article in journal (Refereed)
    Abstract [en]

    The wide distribution of diverse nitrogenase (nifH) genes affiliated with those of heterotrophic bacteria in marine and estuarine waters indicates ubiquity and an ecologically relevant role for heterotrophic N-2-fixers (diazotrophs) in aquatic nitrogen (N) cycling. However, the lack of cultivated representatives currently precludes an evaluation of their N-2-fixing capacity. In this study, microoxic or anoxic N-free media were inoculated with estuarine Baltic Sea surface water to select for N-2-fixers. After visible growth and isolation of single colonies on oxic plates or in anoxic agar tubes, nifH gene amplicons were obtained from 64 strains and nitrogenase activity, applying the acetylene reduction assay, was confirmed for 40 strains. Two strains, one Gammaproteobacterium affiliated with Pseudomonas and one Alphaproteobacterium affiliated with Rhodopseudomonas were shown to represent established members of the indigenous diazotrophic community in the Baltic Sea, with abundances of up to 7.9x10(4) and 4.7x10(4)nifH copies l(-1) respectively. This study reports media for successful isolation of heterotrophic diazotrophs. The applied methodology and the obtained strains will facilitate future identification of factors controlling heterotrophic diazotrophic activity in aquatic environments, which is a prerequisite for understanding and evaluating their ecology and contribution to N cycling at local and regional scales.

  • 10.
    Farnelid, Hanna
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Riemann, Lasse
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Heterotrophic N2-fixing bacteria: overlooked in the marine nitrogen cycle?2008In: Nitrogen Fixation Research Progress / [ed] Couto G.N., New York: Nova Science Publishers , 2008, p. 409-423Chapter in book (Other academic)
  • 11.
    Farnelid, Hanna
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Tarangkoon, Woraporn
    Hansen, Gert
    Hansen, Per Juel
    Riemann, Lasse
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Putative N-2-fixing heterotrophic bacteria associated with dinoflagellate-Cyanobacteria consortia in the low-nitrogen Indian Ocean2010In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 61, no 2, p. 105-117Article in journal (Refereed)
    Abstract [en]

    Heterotrophic dinoflagellates bearing unicellular cyanobacterial symbionts are common within the order Dinophysiales. However, the ecological role of these symbionts is unclear. Due to the occurrence of such consortia in oceanic waters characterized by low nitrogen concentrations, we hypothesized that the symbionts fix gaseous nitrogen (N-2). Individual heterotrophic dinoflagellates containing cyanobacterial symbionts were isolated from the open Indian Ocean and off Western Australia, and characterized using light microscopy, transmission electron microscopy (TEM), and nitrogenase (nifH) gene amplification, cloning, and sequencing. Cyanobacteria, heterotrophic bacteria and eukaryotic algae were recognized as symbionts of the heterotrophic dinoflagellates. nifH gene sequences were obtained from 23 of 37 (62%) specimens of dinoflagellates (Ornithocercus spp. and Amphisolenia spp.). Interestingly, only 2 specimens contained cyanobacterial nifH sequences, while 21 specimens contained nifH genes related to heterotrophic bacteria. Of the 137 nifH sequences obtained 68% were most similar to Alpha-, Beta-, and Gammaproteobacteria, 8% clustered with anaerobic bacteria, and 5% were related to second alternative nitrogenases (anfH). Twelve sequences from 5 host cells formed a discrete cluster which may represent a not yet classified nifH cluster. Eight dinoflagellates contained only 1 type of nifH sequence (>99% sequence identity) but overall the putative N-2-fixing symbionts did not appear host specific and mixed assemblages were often found in single host cells. This study provides the first insights into the nifH diversity of dinoflagellate symbionts and suggests a symbiotic co-existence of non-diazotrophic cyanobacteria and N-2-fixing heterotrophic bacteria in heterotrophic dinoflagellates.

  • 12.
    Farnelid, Hanna
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of California at Santa Cruz, USA.
    Turk-Kubo, Kendra A.
    University of California at Santa Cruz, USA.
    Zehr, Jonathan P.
    University of California at Santa Cruz, USA.
    Identification of Associations between Bacterioplankton and Photosynthetic Picoeukaryotes in Coastal Waters2016In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, article id 339Article in journal (Refereed)
    Abstract [en]

    Photosynthetic picoeukaryotes are significant contributors to marine primary productivity. Associations between marine bacterioplankton and picoeukaryotes frequently occur and can have large biogeochemical impacts. We used flow cytometry to sort cells from seawater to identify non-eukaryotic phylotypes that are associated with photosynthetic picoeukaryotes. Samples were collected at the Santa Cruz wharf on Monterey Bay, CA, USA during summer and fall, 2014. The phylogeny of associated microbes was assessed through 16S rRNA gene amplicon clone and Illumina MiSeq libraries. The most frequently detected bacterioplankton phyla within the photosynthetic picoeukaryote sorts were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Bacteroidetes. Intriguingly, the presence of free-living bacterial genera in the photosynthetic picoeukaryote sorts could suggest that some of the photosynthetic picoeukaryotes were mixotrophs. However, the occurrence of bacterial sequences, which were not prevalent in the corresponding bulk seawater samples, indicates that there was also a selection for specific OTUs in association with photosynthetic picoeukaryotes suggesting specific functional associations. The results show that diverse bacterial phylotypes are found in association with photosynthetic picoeukaryotes. Taxonomic identification of these associations is a prerequisite for further characterizing and to elucidate their metabolic pathways and ecological functions.

  • 13.
    Farnelid, Hanna
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Calif Santa Cruz, Ocean Sci Dept, Santa Cruz, CA 95064 USA.
    Turk-Kubo, Kendra
    Univ Calif Santa Cruz, USA.
    del Carmen Munoz-Marin, Maria
    Univ Calif Santa Cruz, USA ; Univ Cordoba, Spain.
    Zehr, Jonathan P.
    Univ Calif Santa Cruz, USA.
    New insights into the ecology of the globally significant uncultured nitrogen-fixing symbiont UCYN-A2016In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 77, no 3, p. 125-138Article, review/survey (Refereed)
    Abstract [en]

    Cyanobacterial nitrogen-fixers (diazotrophs) play a key role in biogeochemical cycling of carbon and nitrogen in the ocean. In recent years, the unusual symbiotic diazotrophic cyanobacterium Atelocyanobacterium thalassa (UCYN-A) has been recognized as one of the major diazotrophs in the tropical and subtropical oceans. In this review, we summarize what is currently known about the geographic distribution of UCYN-A, as well as the environmental factors that govern its distribution. In addition, by compiling UCYN-A nifH sequences from the GenBank no. database as well as those from nifH gene amplicon next generation sequencing studies, we present an in-depth analysis of the distribution of defined UCYN-A sublineages (UCYN-A1, UCYN-A2 and UCYN-A3) and identify a novel sublineage, UCYN-A4, which may be significant in some environments. Each UCYN-A sublineage exhibited a remarkable global distribution pattern and several UCYN-A sublineages frequently co-occurred within the same sample, suggesting that if they represent different ecotypes they have overlapping niches. Recently, single cell visualization techniques using specific probes targeting UCYN-A1 and UCYN-A2 and their respective associated eukaryotic partner cells showed that the size of the consortia and the number of UCYN-A cells differed between these 2 sublineages. Combined, the results highlight that UCYN-A sublineages likely have different physiological requirements, which need to be accounted for in future studies. Furthermore, based on our increasing knowledge of the diversity of the UCYN-A lineage, we discuss some of the limitations of currently used cultivation-independent molecular techniques for the identification and quantification of UCYN-A.

  • 14.
    Farnelid, Hanna
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Calif Santa Cruz, USA.
    Turk-Kubo, Kendra
    Univ Calif Santa Cruz, USA.
    Ploug, Helle
    University of Gothenburg.
    Ossolinski, Justin E.
    Woods Hole Oceanog Inst, USA.
    Collins, James R.
    Woods Hole Oceanog Inst, USA;Univ Washington, USA.
    van Mooy, Benjamin A. S.
    Woods Hole Oceanog Inst, USA.
    Zehr, Jonathan P.
    Univ Calif Santa Cruz, USA.
    Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre2019In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 13, no 1, p. 170-182Article in journal (Refereed)
    Abstract [en]

    Sinking particles transport carbon and nutrients from the surface ocean into the deep sea and are considered hot spots for bacterial diversity and activity. In the oligotrophic oceans, nitrogen (N-2)-fixing organisms (diazotrophs) are an important source of new N but the extent to which these organisms are present and exported on sinking particles is not well known. Sinking particles were collected every 6 h over a 2-day period using net traps deployed at 150 m in the North Pacific Subtropical Gyre. The bacterial community and composition of diazotrophs associated with individual and bulk sinking particles was assessed using 16S rRNA and nifH gene amplicon sequencing. The bacterial community composition in bulk particles remained remarkably consistent throughout time and space while large variations of individually picked particles were observed. This difference suggests that unique biogeochemical conditions within individual particles may offer distinct ecological niches for specialized bacterial taxa. Compared to surrounding seawater, particle samples were enriched in different size classes of globally significant N-2-fixing cyanobacteria including Trichodesmium, symbionts of diatoms, and the unicellular cyanobacteria Crocosphaera and UCYN-A. The particles also contained nifH gene sequences of diverse non-cyanobacterial diazotrophs suggesting that particles could be loci for N-2 fixation by heterotrophic bacteria. The results demonstrate that diverse diazotrophs were present on particles and that new N may thereby be directly exported from surface waters on sinking particles.

  • 15.
    Farnelid, Hanna
    et al.
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Öberg, Tomas
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Riemann, Lasse
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Identity and dynamics of putative N-2-fixing picoplankton in the Baltic Sea proper suggest complex patterns of regulation2009In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 1, p. 145-154Article in journal (Refereed)
    Abstract [en]

    Heterocystous filamentous cyanobacteria are regarded as the main N-2-fixing organisms (diazotrophs) in the Baltic Sea. However, some studies indicate that picoplankton may also be important. The aim of this study was to examine the composition of putative diazotrophs in the picoplankton (< 3 mu m) and to identify links to environmental factors. Nitrogenase (nifH) genes were amplified from community DNA by nested PCR, followed by cloning and sequencing. Clone libraries from nine environmental samples collected from the central Baltic Sea (April-October 2003, 3 m depth) and a negative control yielded a total of 433 sequences with an average clone library coverage of 92%. The sequences fell within nifH Clusters I, II and III and formed 15 distinct groups (> 96% amino acid similarity). Most of the sequences (77%) fell into nifH Cluster I (cyanobacteria and alpha-, beta- and gamma-Proteobacteria). However, only 26 sequences were related to cyanobacteria (e. g. Pseudanabaena) and among these no unicellular phylotypes were found. Sequences clustering with alternative nitrogenases (anfH) and Archaea were found in one sample while sequences related to anaerobic phylotypes were found in six samples distributed throughout the season. The identified phylogenetic groups showed covariance with several environmental factors but no strong links could be established. This suggests a variable and complex regulation of diazotrophic groups within Baltic Sea picoplankton.

  • 16.
    Riemann, Lasse
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Farnelid, Hanna
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Steward, Grieg F.
    Nitrogenase genes in non-cyanobacterial plankton: prevalence, diversity and regulation in marine waters2010In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 61, p. 225-237Article in journal (Refereed)
    Abstract [en]

    Marine waters are generally considered to be nitrogen (N) limited and are therefore favourable environments for diazotrophs, i.e. organisms converting atmospheric N-2 into ammonium or nitrogen oxides available for growth. In some regions, this import of N supports up to half of the primary productivity. Diazotrophic Cyanobacteria appear to be the major contributors to marine N-2 fixation in surface waters, whereas the contribution of heterotrophic or chemoautotrophic diazotrophs to this process is usually regarded inconsequential. Culture-independent studies reveal that non-cyanobacterial diazotrophs are diverse, widely distributed, and actively expressing the nitrogenase gene in marine and estuarine environments. The detection of nifH genes and nifH transcripts, even in N-replete marine waters, suggests that N-2 fixation is an ecologically important process throughout the oceans. Because this process is highly sensitive to and inhibited by molecular oxygen (O-2), diazotrophy requires efficient scavenging of intracellular O-2 or growth in environments with low ambient O-2 concentration. Particles with interior low-O-2 micro-zones and oceanic oxygen minimum zones are just 2 potential habitats suitable for N-2 fixation by non-cyanobacterial diazotrophs. Our ignorance about the regulation of N-2 fixation by non-Cyanobacteria in their natural marine environments currently prevents an evaluation of their importance in marine N cycling and budgets. A review of the molecular data on distribution and expression of nifH genes in non-Cyanobacteria suggests that further study of the role of these Bacteria in N cycling at local, regional and global scales is needed.

  • 17.
    Sörenson, Eva
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bertos-Fortis, Mireia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Kremp, Anke
    Finnish Environment Institute, Finland;Leibniz Institute for Baltic Sea Research Warnemunde, Germany.
    Kruget, Karen
    Max Planck Institute for Marine Microbiology, Germany.
    Lindehoff, Elin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Finnish Environment Institute, Finland.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Consistency in microbiomes in cultures of Alexandrium species isolated from brackish and marine waters2019In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 11, no 3, p. 425-433Article in journal (Refereed)
    Abstract [en]

    Phytoplankton and bacteria interactions have a significant role in aquatic ecosystem functioning. Associations can range from mutualistic to parasitic, shaping biogeochemical cycles and having a direct influence on phytoplankton growth. How variations in phenotype and sampling location, affect the phytoplankton microbiome is largely unknown. A high‐resolution characterization of the bacterial community in cultures of the dinoflagellate Alexandrium was performed on strains isolated from different geographical locations and at varying anthropogenic impact levels. Microbiomes of Baltic Sea Alexandrium ostenfeldii isolates were dominated by Betaproteobacteria and were consistent over phenotypic and genotypic Alexandrium strain variation, resulting in identification of an A. ostenfeldii core microbiome. Comparisons with in situ bacterial communities showed that taxa found in this A. ostenfeldii core were specifically associated to dinoflagellate dynamics in the Baltic Sea. Microbiomes of Alexandrium tamarense and minutum, isolated from the Mediterranean Sea, differed from those of A. ostenfeldii in bacterial diversity and composition but displayed high consistency, and a core set of bacterial taxa was identified. This indicates that Alexandrium isolates with diverse phenotypes host predictable, species‐specific, core microbiomes reflecting the abiotic conditions from which they were isolated. These findings enable in‐depth studies of potential interactions occurring between Alexandrium and specific bacterial taxa.

  • 18.
    Turk-Kubo, Kendra A.
    et al.
    Univ Calif Santa Cruz, USA.
    Connell, Paige
    Univ Southern Calif, USA.
    Caron, David
    Univ Southern Calif, USA.
    Hogan, Mary E.
    Univ Calif Santa Cruz, USA.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Calif Santa Cruz, USA.
    Zehr, Jonathan P.
    Univ Calif Santa Cruz, USA.
    In Situ Diazotroph Population Dynamics Under Different Resource Ratios in the North Pacific Subtropical Gyre2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 1616Article in journal (Refereed)
    Abstract [en]

    Major advances in understanding the diversity, distribution, and activity of marine N-2-fixing microorganisms (diazotrophs) have been made in the past decades, however, large gaps in knowledge remain about the environmental controls on growth and mortality rates. In order to measure diazotroph net growth rates and microzooplankton grazing rates on diazotrophs, nutrient perturbation experiments and dilution grazing experiments were conducted using free-floating in situ incubation arrays in the vicinity of Station ALOHA in March 2016. Net growth rates for targeted diazotroph taxa as well as Prochlorococcus, Synechococcus and photosynthetic picoeukaryotes were determined under high (H) and low (L) nitrate:phosphate (NP) ratio conditions at four depths in the photic zone (25, 45, 75, and 100 m) using quantitative PCR and flow cytometry. Changes in the prokaryote community composition in response to HNP and LNP treatments were characterized using 16S rRNA variable region tag sequencing. Microzooplankton grazing rates on diazotrophs were measured using a modified dilution technique at two depths in the photic zone (15 and 125 m). Net growth rates for most of the targeted diazotrophs after 48 h were not stimulated as expected by LNP conditions, rather enhanced growth rates were often measured in HNP treatments. Interestingly, net growth rates of the uncultivated prymnesiophyte symbiont UCYN-Al were stimulated in HNP treatments at 75 and 100 m, suggesting that N used for growth was acquired through continuing to fix N-2 in the presence of nitrate. Net growth rates for UCYN-Al , UCYN-C, Crocosphaera sp. (UCYN-B) and the diatom symbiont Richelia (associated with Rhizosolenia) were uniformly high at 45 m (up to 1.6 +/- 0.5 d(-1)), implying that all were growing optimally at the onset of the experiment at that depth. Differences in microzooplankton grazing rates on UCYN-Al and UCYN-C in 15 m waters indicate that the grazer assemblage preyed preferentially on UCYN-Al. Deeper in the water column (125 m), both diazotrophs were grazed at substantial rates, suggesting grazing pressure may increase with depth in the photic zone. Constraining in situ diazotroph growth and mortality rates are important steps for improving parameterization for diazotrophs in global ecosystem models.

  • 19.
    Turk-Kubo, Kendra A.
    et al.
    University of California, USA.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of California, USA.
    Shilova, Irina N.
    University of California, USA.
    Henke, Britt
    University of California, USA.
    Zehr, Jonathan P.
    University of California, USA.
    Distinct ecological niches of marine symbiotic N2-fixing cyanobacterium Candidatus Atelocyanobacterium thalassa sublineages2017In: Journal of Phycology, ISSN 0022-3646, E-ISSN 1529-8817, Vol. 53, no 2, p. 451-461Article in journal (Refereed)
    Abstract [en]

    A recently described symbiosis between the metabolically streamlined nitrogen-fixing cyanobacterium UCYN-A and a single-celled eukaryote prymnesiophyte alga is widely distributed throughout tropical and subtropical marine waters, and is thought to contribute significantly to nitrogen fixation in these regions. Several UCYN-A sublineages have been defined based on UCYN-A nitrogenase (nifH) sequences. Due to the low abundances of UCYN-A in the global oceans, currently existing molecular techniques are limited for detecting and quantifying these organisms. A targeted approach is needed to adequately characterize the diversity of this important marine cyanobacterium, and to advance understanding of its ecological importance. We present findings on the distribution of UCYN-A sublineages based on high throughput sequencing of UCYN-A nifH PCR amplicons from 78 samples distributed throughout many major oceanic provinces. These UCYN-A nifH fragments were used to define oligotypes, alternative taxonomic units defined by nucleotide positions with high variability. The data set was dominated by a single oligotype associated with the UCYN-A1 sublineage, consistent with previous observations of relatively high abundances in tropical and subtropical regions. However, this analysis also revealed for the first time the widespread distribution of the UCYN-A3 sublineage in oligotrophic waters. Furthermore, distinct assemblages of UCYN-A oligotypes were found in oligotrophic and coastally influenced waters. This unique data set provides a framework for determining the environmental controls on UCYN-A distributions and the ecological importance of the different sublineages.

  • 20.
    Zehr, Jonathan P.
    et al.
    University of California, USA.
    Shilova, Irina N.
    University of California, USA.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of California, USA.
    Muñoz-Marín, Maria del Carmen
    University of California, USA;University of Córdoba, Spain.
    Turk-Kubo, Kendra A.
    University of California, USA.
    Unusual marine unicellular symbiosis with the nitrogen-fixing cyanobacterium UCYN-A2017In: Nature Microbiology, E-ISSN 2058-5276, Vol. 2, no 1, p. 1-10, article id 16214Article in journal (Refereed)
    Abstract [en]

    Nitrogen fixation — the reduction of dinitrogen (N2) gas to biologically available nitrogen (N) — is an important source of N for terrestrial and aquatic ecosystems. In terrestrial environments, N2-fixing symbioses involve multicellular plants, but in the marine environment these symbioses occur with unicellular planktonic algae. An unusual symbiosis between an uncultivated unicellular cyanobacterium (UCYN-A) and a haptophyte picoplankton alga was recently discovered in oligotrophic oceans. UCYN-A has a highly reduced genome, and exchanges fixed N for fixed carbon with its host. This symbiosis bears some resemblance to symbioses found in freshwater ecosystems. UCYN-A shares many core genes with the ‘spheroid bodies’ of Epithemia turgida and the endosymbionts of the amoeba Paulinella chromatophora. UCYN-A is widely distributed, and has diversified into a number of sublineages that could be ecotypes. Many questions remain regarding the physical and genetic mechanisms of the association, but UCYN-A is an intriguing model for contemplating the evolution of N2-fixing organelles.

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