Shiraishi, Fumito

[["dc.bibliographiccitation.firstpage","83"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Geomicrobiology Journal"],["dc.bibliographiccitation.lastpage","94"],["dc.bibliographiccitation.volume","25"],["dc.contributor.author","Shiraishi, Fumito"],["dc.contributor.author","Bissett, Andrew"],["dc.contributor.author","de Beer, Dirk"],["dc.contributor.author","Reimer, Andreas"],["dc.contributor.author","Arp, Gernot"],["dc.date.accessioned","2018-11-07T11:19:58Z"],["dc.date.available","2018-11-07T11:19:58Z"],["dc.date.issued","2008"],["dc.description.abstract","The impact of microbial activity on biofilm calcification in aquatic environments is still a matter of debate, especially in settings where ambient water has high CaCO3 mineral supersaturation. In this study, biofilms of two CO(2-)degassing karst-water creeks in Germany, which attain high calcite supersaturation during their course downstream, were investigated with regard to water chemistry of the biofilm microenvironment. The biofilms mainly consisted of filamentous cyanobacteria (Phormidium morphotype) and heterotrophic bacteria (including sulfate-reducing bacteria), which affect the microenvironment and produce acidic exopolymers. In situ and ex situ microelectrode measurements showed that a strong pH increase, coupled with Ca2+ consumption, occurred in light conditions at the biofilm surface, while the opposite occurred in the dark. Calcite supersaturation at the biofilm surface, calculated from ex situ Ca2+ and CO32- microelectrode measurements, showed that photosynthesis resulted in high omega values during illumination, while respiration slightly lowered supersaturation values in the dark, compared to values in the water column. Dissociation calculation demonstrated that the potential amount of Ca2+ binding by exopolymers would be insufficient to explain the Ca2+ loss observed, although Ca2+ complexation to exopolymers might be crucial for calcite nucleation. No spontaneous precipitation occurred on biofilm-free limestone substrates under the same condition, regardless of high supersaturation. These facts indicate that photosynthesis is a crucial mechanism to overcome the kinetic barrier for CaCO3 precipitation, even in highly supersaturated settings."],["dc.identifier.doi","10.1080/01490450801934888"],["dc.identifier.isi","000254214400002"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/55419"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1521-0529"],["dc.relation.issn","0149-0451"],["dc.title","Photosynthesis, respiration and exopolymer calcium-binding in biofilm calcification (Westerhfer and deinschwanger creek, germany)"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1159"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Limnology and Oceanography"],["dc.bibliographiccitation.lastpage","1168"],["dc.bibliographiccitation.volume","53"],["dc.contributor.author","Bissett, Andrew"],["dc.contributor.author","de Beer, Dirk"],["dc.contributor.author","Schoon, Raphaela"],["dc.contributor.author","Shiraishi, Fumito"],["dc.contributor.author","Reimer, Andreas"],["dc.contributor.author","Arp, Gernot"],["dc.date.accessioned","2018-11-07T11:15:41Z"],["dc.date.available","2018-11-07T11:15:41Z"],["dc.date.issued","2008"],["dc.description.abstract","Epilithic and endolithic biofilms were found to control the formation of stromatolites in karst-water creeks. We used microsensors to determine the influence of biological processes on chemical conditions within the microenvironment of crystal nucleation sites: the stromatolite surface. Phototrophic members of the biofilms consisted of mainly cyanobacteria and diatoms. Oxygen, pH, calcium, and carbonate concentration microprofiles at the stromatolite surface and boundary layer showed a strong diurnal rhythm of calcium carbonate precipitation. During illumination, photosynthesis caused oxygen production, a marked increase in pH and CO32- concentrations, and a decrease in Ca2+ concentration at the stromatolite surface due to calcium carbonate precipitation. The opposite occurred in the dark, indicating decalcification. Calcite was approximately 16 times oversaturated in the bulk water, photosynthesis induced an increase of the supersaturation to > 27 at the stromatolite surface under illumination, and respiration induced a decrease of the supersaturation to < 10 in the dark. Photosynthetically stimulated calcium carbonate precipitation was confirmed by radioactive isotope ( Ca-45(2+)) uptake studies. Over a 24 h light : dark cycle, biofilms showed net calcification. Biotic activity within the stromatolite has a large effect on conditions at its surface and, therefore, contributes considerably to the stromatolite precipitation process."],["dc.identifier.doi","10.4319/lo.2008.53.3.1159"],["dc.identifier.isi","000256498900024"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/54423"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1939-5590"],["dc.relation.issn","0024-3590"],["dc.title","Microbial mediation of stromatolite formation in karst-water creeks"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","6306"],["dc.bibliographiccitation.issue","20"],["dc.bibliographiccitation.journal","Applied and Environmental Microbiology"],["dc.bibliographiccitation.lastpage","6312"],["dc.bibliographiccitation.volume","74"],["dc.contributor.author","Bissett, Andrew"],["dc.contributor.author","Reimer, Andreas"],["dc.contributor.author","de Beer, Dirk"],["dc.contributor.author","Shiraishi, Fumito"],["dc.contributor.author","Arp, Gernot"],["dc.date.accessioned","2018-11-07T11:10:16Z"],["dc.date.available","2018-11-07T11:10:16Z"],["dc.date.issued","2008"],["dc.description.abstract","Ex situ microelectrode experiments, using cyanobacterial biofilms from karst water creeks, were conducted under various pH, temperature, and constant-alkalinity conditions to investigate the effects of changing environmental parameters on cyanobacterial photosynthesis-induced calcification. Microenvironmental chemical conditions around calcifying sites were controlled by metabolic activity over a wide range of photosynthesis and respiration rates, with little influence from overlying water conditions. Regardless of overlying water pH levels (from 7.8 to 8.9), pH at the biofilm surface was approximately 9.4 in the light and 7.8 in the dark. The same trend was observed at various temperatures (4 C and 17 C). Biological processes control the calcium carbonate saturation state (Omega) in these and similar systems and are able to maintain Omega at approximately constant levels over relatively wide environmental fluctuations. Temperature did, however, have an effect on calcification rate. Calcium flux in this system is limited by its diffusion coefficient, resulting in a higher calcium flux (calcification and dissolution) at higher temperatures, despite the constant, biologically mediated pH. The ability of biological systems to mitigate the effects of environmental perturbation is an important factor that must be considered when attempting to predict the effects of increased atmospheric partial CO2 pressure on processes such as calcification and in interpreting microfossils in the fossil record."],["dc.description.sponsorship","German Research Foundation [DFGFOR 571]"],["dc.identifier.doi","10.1128/AEM.00877-08"],["dc.identifier.isi","000259985300017"],["dc.identifier.pmid","18689512"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/53177"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","0099-2240"],["dc.title","Metabolic microenvironmental control by photosynthetic biofilms under changing macroenvironmental temperature and pH conditions"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","91"],["dc.bibliographiccitation.issue","1-2"],["dc.bibliographiccitation.journal","Palaeogeography, Palaeoclimatology, Palaeoecology"],["dc.bibliographiccitation.lastpage","106"],["dc.bibliographiccitation.volume","262"],["dc.contributor.author","Shiraishi, Fumito"],["dc.contributor.author","Reimer, Andreas"],["dc.contributor.author","Bissett, Andrew"],["dc.contributor.author","de Beer, Dirk"],["dc.contributor.author","Arp, Gernot"],["dc.date.accessioned","2018-11-07T11:15:00Z"],["dc.date.available","2018-11-07T11:15:00Z"],["dc.date.issued","2008"],["dc.description.abstract","Cyanobacteria-dominated biofilms in a CO(2)-degassing karst-water creek (Westerhofer Bach, Germany) were investigated with regard to the effects of microbial activity on CaCO(3) precipitation, water chemistry of micro- and macroenvironments, stable isotopic records, and tufa fabric formation. Ex situ microelectrode measurements of pH, O(2), and Ca(2+) and CO(3)(2-) revealed that annually laminated calcified biofilms composed mainly of filamentous cyanobacteria (tufa stromatolites) strongly induced CaCO(3) precipitation by photosynthesis under illumination, but inhibited precipitation by respiration in the dark. In contrast, endolithic cyanobacterial biofilms and mosses did not cause photosynthesis-induced precipitation under experimental conditions. No spontaneous precipitation occurred on bare limestone substrates, despite high calcite supersaturation of the ambient water. Mass balance calculations suggest that biofilm photosynthesis was responsible for 10-20% of Ca(2+) loss in the creek, while the remaining Ca(2+) loss derived from physicochemical precipitation on branches, leaves and as fine-grained calcite particles. Neither analysis of bulk water chemistry nor oxygen nor carbon stable isotopic records of the tufa stromatolites confirmed photosynthetic effects, despite the evident photosynthesis-induced calcite precipitation. Oxygen stable isotopic values reflected seasonal changes in water temperature, and carbon stable isotope values probably recorded carbon isotopic composition of dissolved inorganic carbon in the creek water. Annual lamination and fabric formation of the tufa stromatolites is suggested to vary with photosynthesis-induced calcite precipitation rates that are affected by temperature dependency of diffusion coefficients. Photosynthesis-induced precipitation resulted in encrusted cyanobacterial sheaths, reflecting syntaxial overgrowth of microcrystalline cyanobacterial tubes by microspar, instead of microcrystalline sheath impregnation, which was previously suggested as an indicator of photosynthesis-induced precipitation. Therefore, sheath impregnation or encrustation by CaCO(3) cannot be used to distinguish photosynthesis-induced from physicochemically-induced CaCO(3) precipitation. (C) 2008 Elsevier B.V. All rights reserved."],["dc.identifier.doi","10.1016/j.palaeo.2008.02.011"],["dc.identifier.isi","000257011900007"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/54274"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","0031-0182"],["dc.title","Microbial effects on biofilm calcification, ambient water chemistry and stable isotope records in a highly supersaturated setting (Westerhofer Bach, Germany)"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","103"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Journal of Microbiological Methods"],["dc.bibliographiccitation.lastpage","108"],["dc.bibliographiccitation.volume","75"],["dc.contributor.author","Shiraishi, Fumito"],["dc.contributor.author","Zippel, Barbara"],["dc.contributor.author","Neu, Thomas R."],["dc.contributor.author","Arp, Gernot"],["dc.date.accessioned","2018-11-07T11:11:36Z"],["dc.date.available","2018-11-07T11:11:36Z"],["dc.date.issued","2008"],["dc.description.abstract","Modified protocols of fluorescence in situ hybridization (FISH) and catalyze reporter deposition fluorescence in situ hybridization (CARD-FISH) were developed in order to detect bacteria in situ in calcified stromatolite biofilms. Smooth, well-preserved thin sections of calcified biofilms (similar to 5 mu m thin, vertical sectioning of -1 cm deep) were obtained by cryo-sectioning using the adhesive tape-stabilization technique. A modified hybridization buffer was applied during hybridization to prevent calcite dissolution as well as false binding of oligonucleotide probes to the charged mineral surfaces. Particularly, bright and specific CARD-FISH signals allowed the detection of bacteria in intensively calcified biofilms even at low magnification, which is suitable for investigating millimeter- to centimeter-scale vertical distribution patterns of bacteria. (C) 2008 Elsevier B.V. All Fights reserved."],["dc.description.sponsorship","German Research Foundation [DFG-FOR 571; AR 335/5]"],["dc.identifier.doi","10.1016/j.mimet.2008.05.015"],["dc.identifier.isi","000259426600015"],["dc.identifier.pmid","18571259"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/53473"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","0167-7012"],["dc.title","In situ detection of bacteria in calcified biofilms using FISH and CARD-FISH"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","PII 933983816"],["dc.bibliographiccitation.firstpage","135"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Geomicrobiology Journal"],["dc.bibliographiccitation.lastpage","148"],["dc.bibliographiccitation.volume","28"],["dc.contributor.author","Okumura, Tomoyo"],["dc.contributor.author","Takashima, Chizuru"],["dc.contributor.author","Shiraishi, Fumito"],["dc.contributor.author","Nishida, Shin"],["dc.contributor.author","Yukimura, Kise"],["dc.contributor.author","Naganuma, Takeshi"],["dc.contributor.author","Koike, Hiroko"],["dc.contributor.author","Arp, Gernot"],["dc.contributor.author","Kano, Akihiro"],["dc.date.accessioned","2018-11-07T09:01:20Z"],["dc.date.available","2018-11-07T09:01:20Z"],["dc.date.issued","2011"],["dc.description.abstract","An aragonite travertine at Nagano-yu hot spring, SW Japan, exhibits clear sub-millimeter-order lamination that resembles ancient ministromatolites. Thirty-three hours of continuous observation showed that the lamination is formed daily with no changes in physicochemical properties except light intensity. Phylotype analysis and fluorescence in situ hybridization indicate that Hydrogenophaga sp. is dominant and concentrated in diurnal layers containing abundant extracellular polymeric substances. Growth of Hydrogenophaga sp. is activated in the daytime, likely due to extracellular polymeric substance production by cyanobacterial photosynthesis. Daytime development of Hydrogenophaga-dominant biofilms, and the concurrent inhibiting effect on aragonite precipitation, explains the daily lamination observed."],["dc.identifier.doi","10.1080/01490451003743275"],["dc.identifier.isi","000287709300004"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/24401"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","0149-0451"],["dc.title","Microbial Processes Forming Daily Lamination in an Aragonite Travertine, Nagano-yu Hot Spring, Southwest Japan"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","157"],["dc.bibliographiccitation.journal","Geochimica et Cosmochimica Acta"],["dc.bibliographiccitation.lastpage","174"],["dc.bibliographiccitation.volume","77"],["dc.contributor.author","Shiraishi, Fumito"],["dc.date.accessioned","2018-11-07T09:14:24Z"],["dc.date.available","2018-11-07T09:14:24Z"],["dc.date.issued","2012"],["dc.description.abstract","Chemical conditions favoring photosynthesis-induced CaCO3 precipitation (PCP) was examined to provide basic knowledge for understanding ancient ocean chemistry that enabled microbial carbonate formation. First, numerical simulations were conducted to examine the property of photosynthetic increase in CaCO3 saturation state (Delta Omega), an indicator for PCP introduced by previous studies. These simulations revealed that Delta Omega attained a high value at high Ca2+ concentration, low ionic strength, and optimum pH and dissolved inorganic carbon (DIC) where a low-DIC effect and CO2/CO32- buffering were insignificant. Second, microelectrode measurements were conducted using cyanobacteria-dominated stromatolite to examine the property of actual PCP. Although Ca2+ concentration and ionic strength similarly affected actual PCP, the influences of pH and DIC were quite different from what was expected from simulations: significant PCP occurred even at high DIC (up to similar to 300 mmol L-1) where the Delta Omega increase was suppressed by CO2/CO32- buffering. Instead, actual PCP reflected the photosynthetically achieved saturation state (Omega(aft)), which is the sum of Delta Omega and initial saturation state (Omega(bef)). Thus, the chemical conditions favoring PCP is an optimum pH-DIC condition where Delta Omega achieves a high value and/or a high pH-DIC condition where Omega(bef) achieves a high value, in addition to a sufficiently high Ca2+ concentration and low ionic strength. The microelectrode measurements also revealed that the photosynthetic pH increase did not always reflect the occurrence and significance of PCP. (C) 2011 Elsevier Ltd. All rights reserved."],["dc.identifier.doi","10.1016/j.gca.2011.11.004"],["dc.identifier.isi","000299010400011"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/27397"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Pergamon-elsevier Science Ltd"],["dc.relation.issn","0016-7037"],["dc.title","Chemical conditions favoring photosynthesis-induced CaCO3 precipitation and implications for microbial carbonate formation in the ancient ocean"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","83"],["dc.bibliographiccitation.lastpage","118"],["dc.contributor.author","Arp, Gernot"],["dc.contributor.author","Bissett, Andrew"],["dc.contributor.author","Brinkmann, Nicole"],["dc.contributor.author","Cousin, Sylvie"],["dc.contributor.author","de Beer, Dirk"],["dc.contributor.author","Friedl, Thomas"],["dc.contributor.author","Mohr, Kathrin I."],["dc.contributor.author","Neu, Thomas R."],["dc.contributor.author","Reimer, Andreas"],["dc.contributor.author","Shiraishi, Fumito"],["dc.contributor.author","Stackebrandt, Erko"],["dc.contributor.author","Zippel, Barbara"],["dc.date.accessioned","2020-05-04T11:31:29Z"],["dc.date.available","2020-05-04T11:31:29Z"],["dc.date.issued","2010"],["dc.description.abstract","To understand mechanisms of tufa biofilm calcification, selected karstwater stream stromatolites in Germany have been investigated with regard to their hydrochemistry, biofilm community, exopolymers, physicochemical microgradients, calcification pattern and lamination. In stream waters, CO2 degassing drives the increase in calcite saturation to maximum values of approximately 10-fold, independent from the initial Ca2+/alkalinity ratio. For the cyanobacteria of tufa biofilms, a culture-independent molecular approach showed that microscopy of resinembedded biofilm thin sections underestimated the actual diversity of cyanobacteria, i.e. the six cyanobacteria morphotypes were opposed to nine different lineages of the 16S rDNA phylogeny. The same morphotype may even represent two genetically distant cyanobacteria and the closest relatives of tufa biofilm cyanobacteria may be from quite different habitats. Diatom diversity was even higher in the biofilm at the studied exemplar site than that of the cyanobacteria, i.e. 13 diatom species opposed to 9 cyanobacterial lineages. The non-phototrophic prokaryotic biofilm community is clearly different from the soil-derived community of the stream waters, and largely composed of flavobacteria, firmicutes, proteobacteria and actinobacteria. The exopolymeric biofilm matrix can be divided into three structural domains by fluorescence lectin-binding analysis. Seasonal and spatial variability of these structural EPS domains is low in the investigated streams. As indicated by microsensor data, biofilm photosynthesis is the driving mechanism in tufa stromatolite formation. However, photosynthesis-induced biofilm calcification accounts for only 10-20% of the total CaCa2+ loss in the streams, and occurs in parallel to inorganic precipitation driven by CO2-degassing within the water column and on biofilm-free surfaces. Annual stromatolite laminae reflect seasonal changes in temperature and light supply. The stable carbon isotope composition of the laminae is not affected by photosynthesis-induced microgradients, but mirrors that of the bulk water body only reflecting climate fluctuations. Tufa stromatolites with their cyanobacterial-photosynthesis-related calcification fabrics form an analogue to porostromate cyanobacterial stromatolites in fossil settings high in CaCO3 mineral supersaturation but comparatively low in dissolved inorganic carbon. Here, the sum-effect of heterotrophic exopolymerdegradation and secondary Ca2+-release rather decreases calcite saturation, contrary to settings high in dissolved inorganic carbon such as soda lakes."],["dc.identifier.doi","10.1144/SP336.6"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/64602"],["dc.language.iso","en"],["dc.relation.ispartof","Tufas and Speleothems: Unravelling the Microbial and Physical Controls"],["dc.title","Tufa-forming biofilms of German karstwater streams: microorganisms, exopolymers, hydrochemistry and calcification"],["dc.type","book_chapter"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]