Dvoletna študija strukture in sezonske dinamike bakterijske združbe v Tržaškem zalivu (severni Jadran) je pokazala, da je struktura združbe v površinskem sloju različna od pridnene, kljub plitvosti zaliva. Pridnena bakterijska združba je bolj raznolika ter pod vplivom resuspenzije sedimenta. Na hitrost rasti bakterijske združbe v površinskem sloju vpliva temperatura, na strukturo združbe pa rečni vnosi s hranili ter koncentracija klorofila in vrstna setava fitoplanktona. Cvetenje različnih vrst fitoplanktona vpliva na porast Gamaproteobakterij, predvsem Alteromonadaceae, SAR86 in Vibrionaceae, medtem ko se zmanjša prisotnost prevladujoče skupine Alfaproteobakterij - SAR11 in prevladajo vrste iz družine Rhodobacteraceae. Gibanje vodnih mas in vnos sladke vode v površinskem sloju vpliva na razporediteh hranil in vnos alohtonih mikrobnih vrst. Asociacijske mreže, podprte z dolgoročnimi nizi podatkov, omogočajo vpogled v medsebojne povezave in spremembe znotraj mikrobne združbe povezane s klimatskimi spremembami in/ali antropogenimi vplivi. doi:10.1111/1462-2920.12519. http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12519/abstract;jsessionid=67C0A7EA14C461019144A63D24F58EEA.f03t02

Vpliv spremenjenih okoljskih dejavnikov na strukturo in delovanje bakterijske združbe smo testirali v laboratorijskem poizkusu. Vzorce morske vode z naravno mikrobno populacijo smo izpostavili nižjim temperaturam, povišanim koncentracijam fosforja in nižjim koncentracijam kisika. Denaturacijska gradientna gelska elektroforeza in pyrosequencing bakterijskih 16S rRNA genov sta potrdili zmanjšanje števila bakterijskih vrst, kar pa ni spremenilo hitrosti porabe raztopljenega organskega ogljika, kar kaže na funkcionalno redundanco bakterijske združbe. doi: 10.3354/ame01660  http://www.int-res.com/prepress/a01660.html

Obdelava dolgoletne serije podatkov rečnih pretokov, vnosov hranil z rekami, čistilnimi napravami in atmosferske depozicije v Tržaški zaliv je potrdila, da so se vnosi v obdobju od 2003 do 2008 zmanjšali v primerjavi z predhodnimi 5 leti. Spremembe vnosa dušika in fosforja lahko vplivajo na biogeokemične cikle, vrstno sestavo mikroplanktona in prehranske splete. doi: 10.1016/j.ecss.2012.03.005

V obalnih morjih severnega Jadrana povečani vnosi hranil vplivajo na gostoto avtotrofnih celic, kar povzroči nastajanje in kopičenje raztopljenega organskega ogljika, tvorbo organskih delcev (morskega snega) ali večjih agregatov. V tri mesece trajajočem eksperimentu spremljanja sprememb naravne populacije mikroorganizmov po dodatku fosforja je prišlo do kopičenja organske snovi v obliki večjih agregatov. Med številnimi meritvami, je izstopala nizka aktivnost ektohidrolaz na agregatih, kar onemogoča učinkovito razgradnjo in vpliva na regeneracijo fosforja. doi: 10.1016/j.scitotenv.2013.10.040. Raziskava je bila izvedena v sklopu mednarodnega projekta CREICO v sodelovanju z laboratorijem prof. dr. F. Azama, Scripps Inštitut za Oceanografijo (SIO), UC San Diego, ZDA.

Obstajajo različne teorije o tvorbi sluzastih makroagregatov. Kemična sestava in vrstna sestava mikroorganizmov v makroagregatih je zelo raznolika, elektronski posnetki pa nakazujejo zapletene strukture in tesne medsebojne povezave, t.i. »honeycomb strukture«. Procesi nastajanja in vloge mikroorganizmov v/na organskih delcih različnih velikosti so v veliki meri neznani, kot tudi pretvorbe od makrogela v koloidno fazo. doi: 10.3354/ame01447

Bakterije in zooplankton predstavljajo pomembno komponento v pelaški prehranski verigi, v procesih kroženja hranil in trofičnih povezav. Zooplankton predstavlja organsko bogata mikrookolja, ki omogočajo hitro rast bakterij. V publikaciji je podan pregled literature in predstavljeni različni vidiki povezav bakterij z zooplanktonom in možnosti bodočih raziskav na tem področju. doi:10.3354/ame01424.

V zadnjih desetletjih je masovno pojavljanje meduz v obalnih morjih obsežno in pogosto. V mediteranskem morju so prisotne vrste klobučnjaških meduz Aurelia aurita s.l., Pelagia noctiluca in Rhizostoma pulmo. Meduze imajo malo naravnih predatorjev, zato njihovo odmrlo tkivo predstavlja organsko bogat substrat, ki spodbudi hitro rast in spremeni sestavo bakterijske združbe. V zadnji nekaj letih smo izvedli in situ eksperimente z različnimi vrstami meduz in v različnih ekosistemih, v Tržaškem zalivu (S Jadran), Velikem jezeru na Mljetu (J Jadran) in Gelendziku (Črno morje). 

Razgradnja beljakovinsko bogatega substrata povzroča kopičenje amonija in fosforja in znižanje koncentracij kisika v okolju. doi: 10.1007/s10750-010-0223-xhttp://dx.doi.org/10.1007/s10750-010-0223-x

Rezultati analiz sekvenc bakterijskih izolatovin kot tudi sekvenc celotne bakterijske družbe izoliranih iz eksperimentalnih steklenic z meduznim substratom kažejo na spremembe od Alfaproteobakterij v Gamaproteobakterij in Flavobakterije, ter prevlado bakterij iz družin Pseudoalteromonadaceae in Vibrionaceae. doi: 10.1371/journal.pone.0039274. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039274

Meduze izkazujejo izrazito vertikalno migracijo tekom dneva, kar je povezano s prehranskimi navadami. Trofične povezave želatinoznega planktona smo proučevali v velikih eksperimentalnih posodah in vplive manjših plenilcev, z dodatkom radioaktivno označenih mikroorganizmov (Malej in sod. 2008). Naši rezultati potrjujejo kaskadni učinek na mikrobno avtotrofno in heterotrofno populacijo. (Turk in sod. 2008)

Raziskave v zadnjih letih kažejo, da se kopičijo velike količine mikroskopsko majhnih delcev plastike, t.i. mikro- in nanoplastike v področjih močnih tokov v oceanih, morjih, na obalah in na morskem dnu. Čeprav posledice izpostavljanju plastiki niso povsem raziskane, dosedanje študije kažejo, da pri filtratorskih organizmih, kot so morske školjke, pride do prenosa onesnažila iz prebavil v obtok. Alternativa številnim okoljskim problemom je zmanjševanje količin uporabe sintetične plastike in nadomeščanje lete z novimi bio-razgradljivimi materiali. Uporaba tovrstne plastike za izdelavo številnih izdelkov različne uporabe, zahteva dodatne teste in proučevanja. http://www.ciesm.org/online/archives/abstracts/pdf/40/index.php.

Morsko okolje je prejemnik velike količine onesnažil iz številnih virov človekovega izvora. Veljavna zakonodaja se osredotoča predvsem na tveganja, ki jih povzročajo posamezna onesnažila, vendar v okolju vedno nastopajo raznolike mešanice onesnažil, pri katerih je učinek lahko različen od seštevka učinkov posameznih snovi. V medlaboratorijskem testu je sodelovalo 16 laboratorijev, kjer smo testirali vpliv mešanice 14-ih oziroma 19-ih onesnažil ( pesticdov, elementov v sledovih, ogljikovodikov, in drugih) s 35 različnimi biotesti na 11 vrstah organizmov različnih trofičnih nivojev. doi: 10.1093/toxsci/kfu118 http://toxsci.oxfordjournals.org/content/early/2014/06/23/toxsci.kfu118.abstract?sid=d8381fd4-bf03-4904-92c7-b67ce34bb084

Mikroskopi različnih povečav od navadne lupe do elektronskih mikroskopov omogočajo opazovanje nenavadnih, eksotičnih struktur rastlin in živali. Od prvih mikroskopskih risb trgovca z blagom van Leeuwenhoeka je minilo nekaj stoletij, vendar ostaja želja »videti nevidno« nespremenjena. Sodobni mikroskopi omogočajo opazovanja živih organizmov in služijo kot nepogrešljiv pripomoček v znanosti za boljše poznavanje struktur in razumevanje procesov, tako v medicini kot drugih naravoslovnih disciplinah. Izreden napredek predstavlja digitalna fotografija, ki odpira nova poglavja v svetu fotografije in dokumentacije. Fotoaparati z različnimi objektivi in dodatki omogočajo fotografiranje pod velikimi povečavami, vendar le do določene meje. Za proučevanje organizmov manjših od mili-, mikro- in nanometra, uporabljamo mikroskope, na katere pritrdimo digitalno kamero ali fotoaparat.

Pionir na področju fotomikroskopije je bil Roman Vishniac, velik ljubitelj narave, ki je fotografiral živa bitja v gibanju in naredil prve barvne mikrofotografije. Na področju biologije se je specializiral za morsko mikrobiologijo, fiziologijo bičkarjev, s polarizacijsko svetlobo opazoval posamezne celične strukture, organele, molekule in celo aminokisline, kar je objavil v svoji knjigi fotografij »Building blocks of life; proteins, vitamins, and hormones: Seen through the microscop”. Kdo ne pozna vsaj ene od 5000 mikroskopskih slik snežink mikrofotografa Wilsona Bentleya. V slovenskem prostoru je z veliko mero potrpežljivosti in strokovnosti fotografiral morske mikroorganizme v vodi, na morskem dnu ali kopnem fotograf Marjan Richter in del svojega obsežnega opusa objavil v knjigi Naše morje. V večini primerov pa mikrofotografije uporabljamo za raziskovalne namene, umetniški pridih dobijo, na nekaterih tekmovanjih naravoslovne mikrofotografije, ki jih prirejajo veliki proizvajalci mikroskopov, fotoaparatov in druge optične opreme.

The potential link between the microbial dynamics and the environmental parameters was investigated in a semi-enclosed and highly dynamic coastal system (Gulf of Trieste, northern Adriatic Sea). Our comprehensive 2-year time-series study showed that despite the shallowness of this area, there was a significant difference between the surface and the bottom bacterial community structure. The bottom bacterial community was more diverse than the surface one and influenced by sediment re-suspension. The surface seawater temperature had a profound effect on bacterial productivity, while the bacterial community structure was more affected by freshwater-borne nutrients and phytoplankton blooms. Our results propose the importance of the water mass movements as drivers of freshwater-borne nutrients and of allochthonous microbial taxa. This study emphasizes the prediction power based on association networks analyses that are fed with long-term measurements of microbial and environmental parameters. doi:10.1111/1462-2920.12519. http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12519/abstract;jsessionid=67C0A7EA14C461019144A63D24F58EEA.f03t02

In order to obtain insights into the coupling between community composition, diversity and community function, bacterioplankton assemblages from the northern Adriatic Sea were exposed to increasing environmental pressure (decrease of temperature, the addition of phosphorous and the decrease of oxygen level) in continuous seawater cultures to construct communities differing in composition and diversity. Denaturing gradient gel electrophoresis and pyrosequencing of bacterial 16S rRNA genes showed reductions in bacterial diversity. Nevertheless, no differences in the ability to exploit dissolved organic carbon  were found for the acquired communities relative to the inoculum, indicating that the bacterial communities were functionally redundant. doi: 10.3354/ame01660  http://www.int-res.com/prepress/a01660.html

The episodic hyperproduction of mucilage macroaggregates in the northern Adriatic Sea creates an important site for the accumulation, transformation, and degradation of organic matter. The structure and function of macroaggregate components in relation to their macrogel and colloidal fractions was discussed in paper doi: 10.3354/ame01447. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies, has profound implications for the function of these complex communities. High resolution electron microscopy showed a very complex structure, a honeycomb-like structure of the mucus macroagregates. The majority of carbohydrate and protein macroaggregate pools are usually degradable, while the great majority of lipids can be preserved.

The discrepancies between bacterial ectoenzyme potential activities and biogeochemical degradation processes were further intensively studied in 64-day mesocosms experiment. Extensive biogeochemical parameters, processes and community composition were measured after addition of inorganic phosphorous to natural microbial population. Variation in bacterial ectohydrolase activities on aggregates, regulating the rates of particulate →dissolved organic matter transition as well as dissolved polymer hydrolysis, suggests that this could be a bottleneck in phosphorous  regeneration. This could be another regulatory step, in addition to alkaline phosphates (APase), in the microbial regulation of P cycle and the coupling between C and P cycles. doi: 10.1016/j.scitotenv.2013.10.040; http://www.sciencedirect.com/science/article/pii/S0048969713011844

Bacteria and metazoan zooplankton (mainly crustaceans) are often viewed as two separate functional groups in the pelagic food webs indirectly linked via nutrient cycling and trophic cascades. Zooplankton bodies are organic-rich microenvironments that support fast bacterial growth. Our review publication focuses on zooplankton as an important and unique microhabitat for many pelagic bacteria, onthe interactions between these two components, and points to the future challenges and opportunities in this research field. doi: 10.3354/ame01424.

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the affected regions and the common bloom - forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. We conducted several in situ jellyfish - enrichment experiment with different jellyfish species and in different jellyfish occurring ecosystems (The Gulf of Trieste – northern Adriatic, The Big Lake on the Mljet Island – southern Adriatic, the Gelendzik - Black Sea). The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients, as well as oxygen concentrations. doi: 10.1007/s10750-010-0223-x.

Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bio available to ‘jellyfish - associated’ and ‘free - living’ bacteria, and triggers shifts in bacterial population dynamics and composition. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed shift from Alphaproteobacteria to Gammaproteobacteria and Flavobacteria and the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. doi: 10.1371/journal.pone.0039274 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039274,

The impact of the scyphomedusa Aurelia sp. on planktonic assemblages was experimentally studied in enclosures incubated in situ in the sea lake of Mljet Island (southern Adriatic). A reduction in abundance for small calanoid and cyclopoid copepods, copepodites, nauplii and ciliates was observed in the presence of Aurelia sp. In addition to direct predatory pressure, Aurelia sp. exerted an indirect cascading effect on autotrophic and heterotrophic microbial plankton. The top-down effect of predation, along with material release by Aurelia sp. results in increases in microbial biomass and production. (Turk et al. 2008)

Populations of Noctiluca scintillans were compared in the northeastern-central Black Sea and the northern Adriatic Sea. Seasonal changes in cell abundance demonstrated a regular annual maximum with the peak in May–June with additional sporadic peaks in other seasons. The concentration of the eggs of Calanus euxinus was significantly positively correlated with abundance of Noctiluca and the possible effect of a high concentration of copepod eggs on the growth of Noctiluca is discussed and that its outbursts during the peak period are controlled by the wind. http://dx.doi.org/10.1016/j.hal.2014.01.004
Response of microbes to anthropogenic impacts and different organic pollutants

Because of their positive characteristics and benefits, bioplastic or biodegradable polymers are considered to be a viable alternative to conventional plastics. The biodegradation of bioplastic in the presence of different microbes was evaluated under diverse conditions in laboratory and marine environment. http://www.ciesm.org/online/archives/abstracts/pdf/40/index.php.

The risk posed by complex chemical mixtures in the environment to wildlife and humans is increasingly debated, but has been rarely tested under environmentally relevant scenarios. To address this issue, two mixtures of 14 or 19 substances of concern (pesticides, pharmaceuticals, heavy metals, polyaromatic hydrocarbons a surfactant, and a plasticizer), each present at its safety limit concentration imposed by the European legislation, were prepared and tested for their toxic effects. The effects of the mixtures were assessed in 35 bioassays, based on 11 organisms representing different trophic levels. A consortium of 16 laboratories was involved in performing the bioassays. doi: 10.1093/toxsci/kfu118; http://toxsci.oxfordjournals.org/content/early/2014/06/23/toxsci.kfu118.abstract?sid=d8381fd4-bf03-4904-92c7-b67ce34bb084