Co-Existence and niche differentiation of sulfur oxidizing bacteria in marine environments

Reduced sulfur compounds and sulfur-oxidizing prokaryotes (SOP) are widely distributed in the marine environment. Diverse microbial lineages thrive on the oxidation of reduced sulfur. They co-exist successfully by the adaptive radiation into different physiological and ecological niches. However, the factors determining this differentiation and SOP distribution are largely unknown. Environmental factors, like pH, temperature and salinity, as well as the physiological capabilities of different SOPs for sulfur-oxidation and carbon assimilation likely govern the niche-differentiation. Therefore, as part of multiple collaborative studies, I studied the influence of substrate quality and availability on structuring sulfur-oxidizing microbial communities in different marine habitats. First, the role of elemental sulfur (S0), in particular cyclooctasulfur (S8), as substrate for SOPs in marine benthic habitats was examined (Chapter II). We observed a specific association between Sulfurimonas/Sulfurovum-related Epsilonproteobacteria and S0/S8 regardless of the habitat. We propose that substrate quality effects SOP diversity and niche differentiation, and the capability to oxidize S8 probably provides a competitive advantage to the Sulfurimonas/Sulfurovum-group. Moreover, we investigated the diversity and distribution SOPs along gradients of a sulfide, oxygen and light in a highly sulfidic marine karst lake (Lake Rogoznica, Chapter III). The comprehensive analysis of microbial diversity revealed a community shift from phototrophic to chemotrophic sulfur oxidation during holomixis and tight coupling between sulfide and oxygen concentration and the sulfur-oxidizing microbial community in Lake Rogoznica. In two further studies, we explored different aspects of carbon assimilation in hydrothermally influenced habitats dominated by thiotrophic Sulfurimonas/Sulfurovum-related Epsilonproteobacteria. We demonstrated the effects of temperature and/or substrate flux on carbon-isotope fractionation during CO2 assimilation in environmental samples (Chapter IV). Furthermore, we showed that these and other hydrothermal vent associated thiotrophs do not incorporate acetate (Chapter V), despite their heterotrophic potential. Other microorganisms, not involved in oxidative sulfur cycling at hydrothermal vents, showed high activity and growth after the input of organic substrate. In summary, this thesis contributes to the general understanding of microbial ecology in sulfur-rich environments by provides novel insights into diversity and niche in sulfur-oxidizing microbial communities

Qualitative and quantitative research on melanomacrophage centers in fish liver tissue

Makrofagni centri u jetri riba bitan su marker zdravstvenog stanja jedinke te se kao takvi mogu koristiti kao bioindikatori stresa i djelovanja raznih egzogenih tvari na ribe. Zbog relativno jednostavne morfologije tkiva jetre, koja olakšava uočavanje ove vrste degenerativnih promjena tkiva pod svjetlosnim mikroskopom, popularna su tema istraživanja u histopatologiji. Iako su postupci za kvantitativnu i kvalitativnu analizu već uhodani i standardizirani, istraživači su se kroz protekla dva desetljeća osvijestili značajnosti koraka uzorkovanja i poznavanja same biologije istraživane vrste, što oboje značajno utječe na brojnost makrofagnih centara u jetri ribe. U ovom radu pružen je uvid u strukturu i porijeklo makrofagnih centara, moguće uzroke njihovog nastanka i metodologiju rada koja se obično primjenjuje prilikom istraživanja istih.Melanomacrophage centers in the liver of fish are an important marker of health status of individuals and as such can be used as bioindicators of stress and the effects of various exogenous substances on fish. Because of the relatively simple morphology of liver tissue, which facilitates the observation of different types of degenerative changes in it, it is a popular topics of research in histopathology. However, although the procedures for the quantitative and qualitative analysis, is both well known and standardized, the researchers through the last two decades, became more aware of the significance of the sampling step and knowledge about the biology and ecology of the species studied. This is because many natural factors significantly affects the abundance of melanomacrophage centers in the liver of fish. In this review, a brief overview to the structure and origin of melanomacrophage centers is presented, as well as the possible causes of their origin and methodology that is commonly used to explore them

Qualitative and quantitative research on melanomacrophage centers in fish liver tissue

Makrofagni centri u jetri riba bitan su marker zdravstvenog stanja jedinke te se kao takvi mogu koristiti kao bioindikatori stresa i djelovanja raznih egzogenih tvari na ribe. Zbog relativno jednostavne morfologije tkiva jetre, koja olakšava uočavanje ove vrste degenerativnih promjena tkiva pod svjetlosnim mikroskopom, popularna su tema istraživanja u histopatologiji. Iako su postupci za kvantitativnu i kvalitativnu analizu već uhodani i standardizirani, istraživači su se kroz protekla dva desetljeća osvijestili značajnosti koraka uzorkovanja i poznavanja same biologije istraživane vrste, što oboje značajno utječe na brojnost makrofagnih centara u jetri ribe. U ovom radu pružen je uvid u strukturu i porijeklo makrofagnih centara, moguće uzroke njihovog nastanka i metodologiju rada koja se obično primjenjuje prilikom istraživanja istih.Melanomacrophage centers in the liver of fish are an important marker of health status of individuals and as such can be used as bioindicators of stress and the effects of various exogenous substances on fish. Because of the relatively simple morphology of liver tissue, which facilitates the observation of different types of degenerative changes in it, it is a popular topics of research in histopathology. However, although the procedures for the quantitative and qualitative analysis, is both well known and standardized, the researchers through the last two decades, became more aware of the significance of the sampling step and knowledge about the biology and ecology of the species studied. This is because many natural factors significantly affects the abundance of melanomacrophage centers in the liver of fish. In this review, a brief overview to the structure and origin of melanomacrophage centers is presented, as well as the possible causes of their origin and methodology that is commonly used to explore them

Qualitative and quantitative research on melanomacrophage centers in fish liver tissue

Makrofagni centri u jetri riba bitan su marker zdravstvenog stanja jedinke te se kao takvi mogu koristiti kao bioindikatori stresa i djelovanja raznih egzogenih tvari na ribe. Zbog relativno jednostavne morfologije tkiva jetre, koja olakšava uočavanje ove vrste degenerativnih promjena tkiva pod svjetlosnim mikroskopom, popularna su tema istraživanja u histopatologiji. Iako su postupci za kvantitativnu i kvalitativnu analizu već uhodani i standardizirani, istraživači su se kroz protekla dva desetljeća osvijestili značajnosti koraka uzorkovanja i poznavanja same biologije istraživane vrste, što oboje značajno utječe na brojnost makrofagnih centara u jetri ribe. U ovom radu pružen je uvid u strukturu i porijeklo makrofagnih centara, moguće uzroke njihovog nastanka i metodologiju rada koja se obično primjenjuje prilikom istraživanja istih.Melanomacrophage centers in the liver of fish are an important marker of health status of individuals and as such can be used as bioindicators of stress and the effects of various exogenous substances on fish. Because of the relatively simple morphology of liver tissue, which facilitates the observation of different types of degenerative changes in it, it is a popular topics of research in histopathology. However, although the procedures for the quantitative and qualitative analysis, is both well known and standardized, the researchers through the last two decades, became more aware of the significance of the sampling step and knowledge about the biology and ecology of the species studied. This is because many natural factors significantly affects the abundance of melanomacrophage centers in the liver of fish. In this review, a brief overview to the structure and origin of melanomacrophage centers is presented, as well as the possible causes of their origin and methodology that is commonly used to explore them

A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria

Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain un-cultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilotand full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB. (c) 2020 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/

Wind environment evaluation on major town of Malaysia

This study focus on wind flow or wind environment of residential areas in Peninsular Malaysia, Sabah and Sarawak. Natural wind flow is one of the most effective methods to help achieve the energy saving in large cities especially under the tropical climate like Malaysia. The weather in Malaysia is characterized by four monsoon regimes, namely, the southwest monsoon, northeast monsoon and two shorter periods of inter-monsoon seasons. For this study, the data of wind velocity in twentytwo (22) weather station in Malaysia obtained from Meteorological Department and considered in wind environment evaluations. Then that data of wind velocities will convert to 1.5 in height at all measuring points were calculated by using the law. The result compared by Table 2.2 in previous researches (Kubota and Miura et al., 2002). From the study, it was found out, in Malaysia there are only two type of wind. First type is weak wind means that area are discomfort thermal and the second type is comfort range to strong wind means that area are comfort thermal. The minimum value of mean wind speed from 2005 to 2009 is O.mis in mean temperature is over 2C at Sitiawan. For the maximum value of mean wind speed is I .7m/s in average value of mean temperature is 276C at Mersing. Base on results, it can be concluded that when considering wind flow at a residential area, terrace housing is not a suitable option for towns located on the south of the Peninsular. It was prefer for high-rise building because it was considered this location of towns was weak wind condition. On the other hand, the major towns exclude the south of the Peninsular including Sabah and Sarawak, they was under the comfort thermal. So, terrace housing or high-rise building is suitable option

Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

Metal-sulfides are wide-spread in marine benthic habitats. At deep-sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene-based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate-reducing Nitrospirae and sulfide-oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr-clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide-oxidizers potentially facilitating metal-sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitat

Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters

Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light‐independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high‐resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 μM O2·h−1. Single‐cell analyses of lake water incubated with 13CO2 in the dark revealed that Chromatium okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40% of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single‐cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments but also that organisms typically considered strict anaerobes may be involved