Martin W. Hahn

• Professor (Associate), PhD
• Associated Professor at University of Innsbruck, Mondsee, Austria

Within a citizen science project, 112 freshwater habitats in Austria were sampled to get bacterial cultures belonging to the genus Aquirufa using a strategy for targeted isolation. We focused on these bacteria because they are widespread and represent typical freshwater bacteria and, furthermore, the typic red pigmentation facilitates preselection....

During a citizen science project, four freshwater habitats in a riparian forest restoration area in Salzburg, Austria, were sampled. The primary aim was to obtain bacterial strains of the genus Aquirufa, a group of typical and widespread freshwater bacteria. Numerous pure cultures of Aquirufa strains could be obtained, three of them originating fro...

Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predat...

Implications of geographic separation and temporal dynamics on the evolution of free-living bacterial species are widely unclear. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world provides an unprecedented opportunity for such investigations. Here we exploited publicly av...

Understanding intricate microbial interactions in the environment is crucial. This is especially true for the relationships between nutrients and bacteria, as phosphorus, nitrogen and organic carbon availability are known to influence bacterial population dynamics. It has been suggested that low nutrient conditions prompt the evolutionary process o...

The diversity of bacteria associated with alpine lichens was profiled. Lichen samples belonging to the Umbilicariaceae family, commonly known as rock tripe lichens, were gathered from two distinct alpine fellfields: one situated on Mt. Brennkogel located in the Eastern European Alps (Austria), and the other on Mt. Stanley located in the Rwenzori mo...

Strains LEOWEIH-7CT and LEPPI-3A were isolated from the Leopoldskroner Weiher, a lake located in the city of Salzburg, Austria. 16S rRNA gene similarities and phylogenetic reconstructions with 16S rRNA gene sequences as well as based on genome sequences revealed that the new strains belong to the A. antheringensis branch of the genus Aquirufa. Calc...

Geographic separation is a principal factor for structuring populations of macroorganisms, with important consequences for evolution, by means of processes such as allopatric speciation. For free-living prokaryotes, implications of geographic separation on their evolution are more unclear. The limited phylogenetic resolution of commonly used marker...

We present two strains affiliated with the GKS98 cluster. This phylogenetically defined cluster is representing abundant, mainly uncultured freshwater bacteria, which were observed by many cultivation-independent studies on the diversity of bacteria in various freshwater lakes and streams. Bacteria affiliated with the GKS98 cluster were detected by...

Fourteen strains, all isolated from the surface of freshwater habitats, were genomically, phylogenetically and phenotypically characterized. The strains were obtained from geographically and climatically broadly scattered sites. This included two lakes in Antarctica, one arctic pond located on the Svalbard archipelago (Norway), a tropical habitat l...

Two bacterial strains, 9H-EGSE T and 15D-MOB T , were isolated from small freshwater habitats located near Salzburg, Austria. They showed the highest 16S rRNA sequence similarities of 100% and 99.9%, respectively, with type strains of species of the genus Aquirufa ( Bacteroidota ). Genome-based phylogenetic reconstructions with 119 amino acid seque...

The aerobic primarily chemoorganotrophic actinobacterial strain MWH-Mo1 T was isolated from a freshwater lake and is characterized by small cell lengths of less than 1 µm, small cell volumes of 0.05–0.06 µm ³ (ultramicrobacterium), a small genome size of 1.75 Mbp and, at least for an actinobacterium, a low DNA G+C content of 54.6 mol%. Phylogenetic...

Sil.va.ni.grel'la. N.L. fem. dim. n. Silvanigrella named after Silva nigra the Latin geographic name of the Schwarzwald (Black Forest) mountains located in the south-west of Germany. Proteobacteria / Oligoflexia / Silvanigrellales / Silvanigrellaceae / Silvanigrella The genus Silvanigrella accommodates heterotrophic freshwater bacteria isolated fro...

Die Grundeinheit der Prokaryotensystematik ist der Stamm (engl. strain; im Gegensatz zum taxonomischen Stamm = Phylum). Unter einem solchen Stamm versteht man eine Reinkultur eines Bakteriums oder Archaeons, also eine klonale Kultur, die auf eine einzelne Zelle zurückgeht. Das Konzept der Reinkultur und die Entwicklung der für die Gewinnung solcher...

Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. The faster evolvi...

The actinobacterial strain 15G-AUS-rot T was isolated from an artificial pond located near Salzburg, Austria. The strain showed 16S rRNA gene sequence similarities of 98.7 % to Candidatus Aquiluna rubra and of 96.6 and 96.7 % to the two validly described species of the genus Rhodoluna . Phylogenetic reconstructions based on 16S rRNA gene sequences...

Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. We used a faster...

Allopatric divergence is one of the principal mechanisms for speciation of macro-organisms. Microbes by comparison are assumed to disperse more freely and to be less limited by dispersal barriers. However, thermophilic prokaryotes restricted to geothermal springs have shown clear signals of geographic isolation, but robust studies on this topic for...

The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria , it rarely affiliates with other proteobacterial classes and is frequently not recovered as a m...

Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic ultramicrobacteria that is frequently very abundant (up to 70% of total bacterioplankton) in freshwater habitats across all seven continents. This strain was originally isolated from a shallow Alpine pond characterized by rapid changes in water...

Two bacterial strains, 50A-KIRBA T and 50C-KIRBA T , were isolated from the same freshwater creek located near Salzburg, Austria. They showed 16S rRNA gene sequence similarities to Aquirufa nivalisilvae of 100 and 99.9 %, respectively. A genome-based phylogenetic reconstruction with amino acid sequences of 119 single-copy genes suggested that the n...

Polynucleobacter (Burkholderiaceae, Betaproteobacteria) and Limnohabitans (Comamonadaceae, Betaproteobacteria) are abundant freshwater bacteria comprising large genetic and taxonomic diversities, with species adapted to physico-chemically distinct types of freshwater systems. The relative importance of environmental drivers, i.e., physico-chemistry...

The bacterial strain 53C-WASEF was isolated from a small freshwater ditch located in Eugendorf, Austria. Phylogenetic reconstructions with 16S rRNA gene sequences and genome based, with amino acid sequences obtained from 105 single copy genes, suggested that the strain represents a new genus and a new species within the family Opitutaceae, which be...

Strain 33A1-SZDPT was isolated from a small creek located in Puch, Austria. Strain SP-Ram-0.45-NSY-1T was obtained from a small pond located in Schönramer Moor, Germany. 16S rRNA gene sequence similarities between the type strain of Silvanigrella aquatica, currently the only member of the family Silvanigrellaceae, and strains 33A1-SZDPT and SP-Ram-...

Three actinobacterial strains, 27D-LEPIT, 1B-Mac and 36A-HELLB, were isolated from small standing and running freshwater habitats located in Salzburg, Austria. Phylogenetic reconstructions based on 16S rRNA gene sequences and genome based on concatenated amino acid sequences of 119 single-copy genes referred the three strains within the family Micr...

Metacommunity theory suggests that dispersal is a key driver of diversity and ecosystem functioning in changing environments. The capacity of dispersal to mitigate effects of environmental change might vary among trophic groups, potentially resulting in changes in trophic interactions and food web structure. In a mesocosm experiment, we compared th...

We studied the impact of protist grazing and exudation on the growth and transcriptomic response of the prokaryotic prey species Polynucleobacter asymbioticus. Different single- and multi-species communities of chrysophytes were used to determine a species-specific response to the predators and the effect of chrysophyte diversity. We sequenced the...

Three bacterial strains, 30S-ANTBAC, 103A-SOEBACH and 59G- WUEMPEL, were isolated from two small freshwater creeks and an intermittent pond near Salzburg, Austria. Phylogenetic reconstructions with 16S rRNA gene sequences and, genome based, with amino acid sequences obtained from 119 single copy genes showed that the three strains represent a new g...

Isolation and cultivation of microorganisms enables in combination with cultivation-independent methods comprehensive research on ecology and function of microbes. The availability of cultures provides opportunities for ecophysiological experiments, enables high-quality genome research and represents a mandatory prerequisite for the description of...

Light is a source of energy and an environmental cue that is available in excess in most surface environments. In prokaryotic systems, conversion of light to energy by photoautotrophs and photoheterotrophs is well understood, but the conversion of light to information and the cellular response to that information has been characterized in only a fe...

Zusammenfassung de Im Projekt „Verborgene Welt der Bakterien“ arbeiten über zwei Jahre Schülerinnen und Schüler von sechs Oberstufenklassen von Gymnasien in und um Salzburg mit Mitarbeiterinnen und Mitarbeitern des Forschungsinstitutes für Limnologie, Mondsee der Universität Innsbruck zusammen. Ziel ist es, gemeinsam neue Bakterienstämme aus Gewäss...

Po.ly.nu.cle.o.bac'ter. Gr. adj. polys, many, numerous; L. masc. n. nucleus, a little nut, kernel; N.L. masc. n. bacter, a rod; N.L. masc. n. polynucleobacter, the rod (bacterium) with many nucleoids. Proteobacteria / Betaproteobacteria / Burkholderiales / Burkholderiaceae / Polynucleobacter The genus Polynucleobacter harbors bacteria with distinct...

Six Polynucleobacter (Burkholderiaceae, Betaproteobacteria) strains isolated from different freshwater lakes located across Europe were taxonomically investigated. Phylogenetic analyses based on 16S rRNA gene sequences assigns all six strains to the cryptic species complex PnecC within the genus Polynucleobacter. Analyses of partial glutamine synth...

Strains MWH-EgelM1-30-B4T and MWH-Feld-100T were isolated from the water columns of two freshwater systems. Both strains represent delicate bacteria not easy to work with in laboratory experiments. Phylogenetic analyses of the 16S rRNA genes suggested that both strains were affiliated with the genus Polynucleobacter. Both strains share 16S rRNA gen...

Strain AP-Melu-1000-B4 was isolated from a lake located in the mountains of the Mediterranean island of Corsica (France). Phenotypic, chemotaxonomic and genomic traits were investigated. Phylogenetic analyses based on 16S rRNA gene sequencing referred the strain to the cryptic species complex PnecC within the genus Polynucleobacter. The strain enco...

The genus Polynucleobacter (family Burkholderiaceae) is phylogenetically subdivided into at least four subclusters. One of those, subcluster PnecC, was recognized as a cryptic species complex. Here we test by comparative genome analyses whether subcluster PnecD, currently solely represented by the species Polynucleobactercosmopolitanus, also repres...

Background In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwater...

The bacterial strain MWH-K35W1(T) was isolated from a permanently anoxic water layer of a meromictic lake located in the Austrian Salzkammergut area. The basically chemo-organoheterotrophic strain was isolated and maintained under aerobic conditions. Phylogenetic analyses of the 16S rRNA gene and the glutamine synthetase gene (glnA) of the strain s...

Strain MWH-Weng1-1T, isolated from an acidic freshwater habitat located in the Wenger Moor, Austria, was characterized by investigating its phenotypic, chemotaxonomic and genomic traits. Phylogenetic analyses based on 16S rRNA gene sequencing placed the strain in the cryptic species complex PnecC within the genus Polynucleobacter. The strain had a...

The unusual chemo-organoheterotrophic proteobacterial strain MWH-Nonnen-W8redT was isolated from a lake located in the Black Forest (Schwarzwald), Germany, by using the filtration-acclimatization method. Phylogenetic analyses based on the 16S rRNA gene sequence of the strain could not provide clear hints on classification of the strain in one of th...

The Betaproteobacteria-Euplotes association is an obligatory symbiotic system involving a monophyletic group of ciliate species and two betaproteobacteria species which can be alternatively present. Recent data showed that this relationship has been established more than once and that several symbiont-substitution events took place, revealing a com...

Importance: Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great impo...

Strain QLW-P1FAT50C-4T, isolated from a shallow acidic freshwater pond located in the Austrian Alps at an altitude of 1300 m, was characterized by investigation of phenotypic, chemotaxonomic and genomic traits. As shown previously, phylogenetic analyses based on 16S rRNA gene sequences place the strain in the cryptic species complex PnecC within th...

Rho.do.lu'na. Gr. n. rhodon the rose, L. fem. n. luna the moon, N.L. fem. n. Rhodoluna red‐colored moon, referring to the red pigmentation and the seemingly selenoid (crescent shape) morphology of the strain. Actinobacteria / Actinobacteria / Micrococcales / Microbacteriaceae / Rhodoluna The genus Rhodoluna represents freshwater bacteria of very sm...

Actinorhodopsin (ActR) is a light-driven outward H? pump. Although the genes of ActRs are widely spread among freshwater bacterioplankton, there are no prior data on their functional expression in native cell membranes. Here, we demonstrate ActR phototrophy in the native actinobacterium. Genome analysis showed that Candidatus Rhodoluna planktonica,...

Genome comparisons based on average nucleotide identity (ANI) values of four strains currently classified as Polynucleobacter necessarius subspecies asymbioticus resulted in ANI values of 75.7-84.1% suggesting that each of those strains represents a separate species. The species P. necessarius was proposed by Heckmann and Schmidt in 1987 to accommo...

Transplantation experiments and genome comparisons were used to determine if lineages of planktonic Polynucleobacter almost indistinguishable by their 16S ribosomal RNA (rRNA) sequences differ distinctively in their ecophysiological and genomic traits. The results of three transplantation experiments differing in complexity of biotic interactions r...

Rhodopsin-encoding microorganisms are common in many environments. However, knowing that rhodopsin genes are present provides little insight into how the host cells utilize light. The genome of the freshwater actinobacterium Rhodoluna lacicola encodes a rhodopsin of the uncharacterized actinorhodopsin family. We hypothesized that actinorhodopsin wa...

Stable isotope mixing models in aquatic ecology require δ13C values for food web end members such as phytoplankton and bacteria, however it is rarely possible to measure these directly. Hence there is a critical need for improved methods for estimating the δ13C ratios of phytoplankton, bacteria and terrestrial detritus from within mixed seston. We...

Sunlight is captured and converted to chemical energy in illuminated environments. Al-though (bacterio)chlorophyll-based photosystems have been characterized in detail, retinal-based photosystems, rhodopsins, have only recently been identified as important mediators of light energy capture and conversion. Recent estimates suggest that up to 70% of...

Complete phylogenetic trees (NJ) of the 16S–23S ITS and the glnA sequences (compare Fig. 1B). Subgroups mentioned in the paper are highlighted by different colours. Strains matching to the RLBH probe F13n targeting the Pantropical clade (Jezbera et al., 2011) and strains matching to PCR primers used for targeting the major branch of the Antarctic c...

Putative range limits of the Pantropical (red), the Antarctic (blue) and the F15 clade (yellow). Range limits deduced from detections by cultivation and cultivation-independent methods are shown as solid lines of a dot (Antarctic clade, region represented by Byers Peninsula and Hope Bay). Hypothetical range limits are shown as dashed lines.

Polynucleobacter strains, geographic origin and Genbank accession numbers of 16S–23S ITS and glnA sequences.

Detection of Polynucleobacter necessarius ssp. asymbioticus subgroups by reverse line blot hybridization (RLBH) in habitats located in Uganda.

Antarctic lakes investigated for the presence of the Antarctic clade.

A pure culture of an actinobacterium previously described as ‘Candidatus Rhodoluna lacicola’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8T represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogene...

The free-living planktonic freshwater bacterium Polynucleobacter necessarius subspecies asymbioticus (>99% 16S rRNA similarity) represents a taxon with a cosmopolitan distribution and apparently ubiquitous occurrence in lentic freshwater habitats. We tested for intra-taxon biogeographic patterns by combining cultivation-independent and cultivation...

There is considerable interest in the pathways by which carbon and growth-limiting elemental and biochemical nutrients are supplied to upper trophic levels. Fatty acids and sterols are among the most important molecules transferred across the plant-animal interface of food webs. In lake ecosystems, in addition to phytoplankton, bacteria and terrest...

Bacteria of the genus Limnohabitans, more precisely the R-BT lineage, have a prominent role in freshwater bacterioplankton communities due to their high rates of substrate uptake and growth, growth on algal-derived substrates and high mortality rates from bacterivory. Moreover, due to their generally larger mean cell volume, compared to typical bac...

Different bacterial strains can have different value as food for heterotrophic nanoflagellates (HNF), thus modulating HNF growth and community composition. We examined the influence of prey food quality using four Limnohabitans strains, one Polynucleobacter strain and one freshwater actinobacterial strain on growth (growth rate, length of lag phase...

Different bacterial strains can have different value as food for heterotrophic nanoflagellates (HNF), thus modulating HNF growth and community composition. We examined the influence of prey food quality using four Limnohabitans strains, one Polynucleobacter strain and one freshwater actinobacterial strain on growth (growth rate, length of lag phase...

Actinorhodopsins (ActRs) are recently discovered proteorhodopsins present in Actinobacteria, enabling them to adapt to a wider spectrum of environmental conditions. Frequently, a large fraction of freshwater bacterioplankton belongs to the acI lineage of Actinobacteria and codes the LG1 type of ActRs. In this paper we studied the genotype variabili...

Among abundant freshwater Betaproteobacteria, only few groups are considered to be of central ecological importance. One of them is the well-studied genus Limnohabitans and mainly its R-BT subcluster, investigated previously mainly by fluorescence in situ hybridization methods. We designed, based on sequences from a large Limnohabitans culture coll...

RLBH detections of probe-defined groups scored as no (no color), weak (light grey color), normal (dark grey color) and strong (black color) across all 161 habitats. For more parameters of habitats see Jezberová et al., 2010; Šimek et al., 2010; Jezbera et al., 2011 and 2012. (DOC)

Table S1. Pairwise comparisons of aligned almost complete 16S rRNA gene sequences of newly isolated Limnohabitans strains and closely related environmental clones and other genera. The similarity is shown in the upper part, the lower part depicts the number of nucleotide differences between sequences. Newly described strains are in bold. Environmen...

The distribution and abundance of Betaproteobacteria and three of its genera - Limnohabitans (R-BT065 lineage), Polynucleobacter (including subclusters Polynucleobacter necessarius and Polynucleobacter acidiphobus/Polynucleobacter difficilis), and Methylophilus - across the epilimnia of 72 limnologically diverse freshwater habitats were investigate...

Background: The bacterial taxon Polynucleobacter necessarius subspecies asymbioticus represents a group of planktonic freshwater bacteria with cosmopolitan and ubiquitous distribution in standing freshwater habitats. These bacteria comprise <1% to 70% (on average about 20%) of total bacterioplankton cells in various freshwater habitats. The ubiqui...

Lack of genes well known from other Burkholderiaceae bacteria. (DOCX)

Abbreviations (DOCX)

Loci used for the multilocus sequence analysis of the eleven F10 lineage strains isolated from Pond-1 (compare Fig. 5). The sequences of Pnuc_1240 were not considered for the calculation of the tree shown in Fig. 5. (DOCX)

Experiment on growth support of Polynucleobacter bacteria by algal exudates. (DOCX)

Bootstrap values obtained in phylogenetic reconstructions using the concatenated amino acid (AA) or nucleotide sequences (nt) of eight housekeeping genes (Fig. 8). For comparison, phylogenetic reconstructions solely based on the 16S rRNA gene sequences of the same set of organisms were performed (tree not shown). Note the strong support for node E...

Current taxonomy of Polynucleobacter bacteria. The genus Polynucleobacter currently harbors five species (Hahn et al., 2009, 2010, 2011a, 2011b, 2012). These five species represent the four Polynucleobacter tribes (PnecA to PnecD) suggested by the taxonomy in Newton et al. (2011). Some of the strains affiliated with the subspecies P. necessarius as...

Results of the assimilation experiments performed with 93 substrates. Substrates that did not support growth of the strain are highlighted in red. Substrates yielding growth efficiencies ≥5% are highlighted in green. Growth efficiencies were not determined for five of the listed substrates. (DOCX)

Loci used for the multilocus sequence analysis shown in Fig. 8. (DOCX)

Genomes and strains considered for the multilocus sequence analysis presented in Fig. 8. (DOCX)

Search for genes involved in adaptations to a planktonic lifestyle. (DOCX)

Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems. The 16S-23S ITS genotype repr...

Principal component analysis plot of environmental and spatial factors, indicating that salinity was the primary gradient across all 33 samples. Concentrations of Na+, K+, Mg2+, SO42− and conductivity significantly positively correlated with salinity (data of all five parameters not shown). The vertical dotted line separates samples with salinities...

Trends of bacterial taxon richness along the investigated salinity gradient by using the DGGE fingerprinting method with primers (341f/907r) and group-specific primers (SUM, SUM-2, etc). SUM: total numbers of bands obtained with phylogenetic primers. SUM-2: the SUM bands number without those of primer sets 2. The number 2–8 indicated the primer set...

Effect of salinity on prokaryotic taxonomic richness in various aquatic ecosystems, except for estuary and fast running environments [6], [7], [9], [10], [21], [22], [53], [54], [55], [56], [57], [58], [59], [60], [61]. (DOC)

Brief descriptions of the lakes investigated in 2005, sorted by salinity. (DOC)