Thermophilic Species Research Articles

An update on novel taxa and revised taxonomic status of bacteria isolated from domestic companion and agricultural animals described in 2023.

With the proliferation of abundant bacterial genomic data comes the recognition of new organisms as well as a better understanding of the relatedness of known bacteria. Recognizing the associated taxonomic changes enhances communication and understanding about the significance of novel organisms and deeper understanding of known pathogens. This review addresses the addition of multiple gastrointestinal bacteria that form the normal microbiota in a variety of animals including honeybees as well as novel bacteria from domestic animals including an alpha-hemolytic Streptococcus species from guinea pigs, two Moraxella spp. from cows and goats, a new Capnocytophaga species from cats, a thermophilic Campylobacter species from pigs, and the new Exercitatus genus in Family Pasteurellaceae. Several revisions to the nomenclature also appeared in 2023 including the change of Clostridium spiroforme, which causes anorexia and diarrhea in domestic rabbits, to Thomasclavelia spiroformis comb. nov. and Mannheimia ovis to Mannheimia pernigra.

Methanothermobacter thermautotrophicus and Alternative Methanogens: Archaea-Based Production.

Methanogenic archaea convert bacterial fermentation intermediates from the decomposition of organic material into methane. This process has relevance in the global carbon cycle and finds application in anthropogenic processes, such as wastewater treatment and anaerobic digestion. Furthermore, methanogenic archaea that utilize hydrogen and carbon dioxide as substrates are being employed as biocatalysts for the biomethanation step of power-to-gas technology. This technology converts hydrogen from water electrolysis and carbon dioxide into renewable natural gas (i.e., methane). The application of methanogenic archaea in bioproduction beyond methane has been demonstrated in only a few instances and is limited to mesophilic species for which genetic engineering tools are available. In this chapter, we discuss recent developments for those existing genetically tractable systems and the inclusion of novel genetic tools for thermophilic methanogenic species. We then give an overview of recombinant bioproduction with mesophilic methanogenic archaea and thermophilic non-methanogenic microbes. This is the basis for discussing putative products with thermophilic methanogenic archaea, specifically the species Methanothermobacter thermautotrophicus. We give estimates of potential conversion efficiencies for those putative products based on a genome-scale metabolic model for M. thermautotrophicus.

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses

Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.

Erstnachweise und Wiederfunde verschollener Stechimmenarten (Hymenoptera Aculeata) in Schleswig-Holstein

Especially intensive collecting activities of the AG Stechimmen Schleswig-Holstein during the years 2016-2022 resulted in the discovery of 37 species of wild bees and aculeate wasps (Hymenoptera Aculeata) that were recorded for the first time in Schleswig-Holstein, Germany, as well as the rediscovery of 19 species that were considered extinct for this region. The newly discovered species are discussed regarding their known distribution in neighbouring regions. In particular, a strong northward dispersal of thermophilic species can be observed, presumably due to climate warming.

Past and current climate as a driver in shaping the distribution of the Longitarsus candidulus species group (Coleoptera: Chrysomelidae).

Longitarsus candidulus (Foudras) is a thermophilic flea beetle species widely distributed in the Mediterranean Basin and associated with Daphne gnidium L. and Thymelaea hirsuta (L.). Longitarsus laureolae Biondi and Longitarsus leonardii Doguet, phylogenetically closely related to L. candidulus, show together a peculiar and rare disjunct distribution along the central-southern Apennines and the Cantabrian-Pyrenean mountain system, respectively. Both are associated with Daphne laureola L. in mesophilic habitats. We used "ecological niche modeling" to infer the Pleistocene dynamics in the distribution of the three flea beetle species and their host plants. We interpreted their current distributions, paying particular attention to the presumed time of species divergence as inferred from recent studies. The differentiation of L. laureolae and L. leonardii from L. candidulus likely represents a response to the marked climatic changes during the Late Pliocene. Such a split was likely associated with a trophic niche shift of the laureolae/leonardii ancestor towards the typically mesophilic host plant D. laureola. The subsequent split between L. laureolae and L. leonardii, possibly due at first to the niche competition, was then boosted by an allopatric divergence during the Middle Pleistocene, likely caused by a large area of low environmental suitability for both species, mainly located between the northern Apennines and the south-western Alps.

Shifts in the altitudinal distribution of alien and native synanthropic plants along roadsides over a 40-year period

Disturbed areas alongside roads shape unique vegetation communities dominated by synanthropic native and alien plant species, facilitated by roads serving as corridors for dispersal, penetration, and integration of synanthropic plants into new areas. We collected presence/absence data for individual species along roads in the Orlické Mountains, Czech Republic, in three time periods during 1970–2010. The distribution of species was mapped using a 1-square-kilometer grid. Analyzing 107 plant species (44 native, 63 alien), we found archaeophyte species favor lower elevations (foothills), while neophytes thrive at higher elevations. Over 40 years, neophyte frequency significantly rose at lower elevations, contrasting the decline at higher elevations, with no marked change in archaeophyte frequency. Native species decline notably at 400–500 m elevations. Some thermophilous native synanthropic species and alien archaeophytes spread from foothills to higher elevations, while some psychrophilic higher-elevation species shift upwards, diminishing at lower elevations. We emphasize human disturbance and global warming as pivotal factors influencing the altitudinal distribution shift in both native and alien plant species.

Chronicles of Kyphosus in the Mediterranean Sea: new records and complete mitogenomes support the scenario of one expanding fish species

The Mediterranean Sea is a biodiversity hotspot, being home to a vast array of marine species. Furthermore, seawater warming is facilitating the arrival and spread of new thermophilic species, posing a severe threat to biodiversity. Among the species currently extending their range and increasing in abundance in Mediterranean waters, sea chubs (genus Kyphosus) are one of the most enigmatic. One challenge arises from the high phenotypic similarity between the two congeneric species documented in the basin: Kyphosus vaigiensis and Kyphosus sectatrix. Their resemblance has often led to identification challenges, resulting in incorrect or omitted species-level classifications. Therefore, despite the growing presence of these fish in the Mediterranean, it remains unclear whether only one or both species are experiencing a demographic increase and range extension. To date, there have been 26 reports of Kyphosus individuals in the Mediterranean Sea, documented in 24 separate papers. Here, we reviewed the history of the genus in the basin and provided 13 new records of these fish from multiple localities along Mediterranean coasts. In addition, we sequenced the entire mitogenomes of two specimens, assessed their phylogenetic relationships with published Kyphosus mitochondrial DNAs from around the world, and conducted detailed morphological and meristic analyses on one of them, allowing us to provide accurate species-level identifications. Our results indicate that K. vaigiensis is the species currently expanding its range in the Mediterranean Sea, while K. sectatrix is still very rare and only sporadically reported. Notably, our mitogenome data indicate that Mediterranean K. vaigiensis individuals most likely came from Atlantic waters, while there is no evidence to support an entrance through the Red Sea or any other anthropogenic vector. Finally, the potential ecological and fishing impacts associated with the proliferation of these fish in the region are discussed.

Seasonal variations in soil microbial community co-occurrence network complexity respond differently to field-simulated warming experiments in a northern subtropical forest

Global warming may reshape seasonal changes in microbial community diversity and co-occurrence network patterns, with significant implications for terrestrial ecosystem function. We conducted a 2-year in situ field simulation of the effects of warming on the seasonal dynamics of soil microbial communities in a northern subtropical Quercus acutissima forest. Our study revealed that warming had no significant effect on the richness or diversity of soil bacteria or fungi in the growing season, whereas different warming gradients had different effects on their diversity in the nongrowing season. Warming also changed the microbial community structure, increasing the abundance of some thermophilic microbial species and decreasing the abundance of some symbiotrophic microorganisms. The co-occurrence network analysis of the microbial community showed that warming decreased the complexity of the intradomain network in the soil bacterial community in the growing and nongrowing seasons but increased it in the fungal community. Moreover, increasing warming temperatures increased the complexity of the interdomain network between bacteria and fungi in the growing season but decreased it in the nongrowing season, and the keystone species in the interdomain network changed with warming. Warming also reduced the proportion of positive microbial community interactions, indicating that warming reduced the mutualism, commensalism, and neutralism of microorganisms as they adapted to soil environmental stress. The factors affecting the fungal community varied considerably across warming gradients, with the bacterial community being significantly affected by soil temperature, MBC, NO3−-N and NH4+-N, moreover, SOC and TN significantly affected fungal communities in the 4 °C warming treatment. These results suggest that warming increases seasonal differences in the diversity and complexity of soil microbial communities in the northern subtropical region, significantly influencing soil dynamic processes regulating forest ecosystems under global warming.

Has climate change over the last ten years caused a banalisation of diatom communities in Cypriot streams?

To unveil possible changes in diatom communities in Cypriot streams over the last ten years or so, we selected samples from the years 2020, 2021, and 2022 for the “recent” dataset (N = 119) and samples from the years 2010 and 2011 for the “historical” dataset (N = 108). Biotic homogenization has become a truly global phenomenon. Here we show that, over the last ten years, in response to increased water temperature, conductivity, and discharge variability due to climate-change, Cypriot stream diatom communities include a higher number of trivial (= widespread, tolerant, and opportunistic), aerial, and thermophilic species, have reduced β-diversity and increased nestedness. Moreover, IndVal analysis shows that indicator species from the historical dataset were characteristic, often relatively rare species, while the indicators of the recent dataset were a group of typical trivial, eutraphentic, and thermophilic species. As is almost always the case, the diatom communities we studied were subjected to multiple stressors, often affecting them in opposite ways. Besides the increase in trivial species, the reduction in β-diversity, and the rise in nestedness mentioned above, the diatom assemblages we studied also showed an increase in α-diversity that could be due to a moderate reduction in nutrients in several sites. High-ecological-integrity ecosystems, such as springs, waterfalls, and dripping rock-walls, in particular springs that were shown to be excellent hydrologic refugia in climates heavily affected by climate change, and the stream sites close to them should be carefully protected, as they can be refugia for sensitive and characteristic species that can recolonize the adjacent streams after adverse climatic events.

Botanical, Chemical, and Pharmacological Characteristics of Carob Tree (Ceratonia Siliqua L)

In Morocco the carob tree (Ceratonia siliqua L.), is scattered in the wild or articificial state throughout the country. It belongs to the Ceasalpiniaceae subfamily of the legume family, is a sclerophyllous, xerophilic, thermophilic, calciclous and heliophilous species. The carob is a Mediterranean medicinal plant, it is characterized by ecological, socio-economic, industrial and ornamental importance. It is an agro-sylvo-pastoral species that can be used for the rehabilitation of degraded soils, thanks to its capacity to adapt to different edapho-climatic conditions. The most important producing countries are Spain, Italy, Morocco, Portugal, Greece, Turkey and Cyprus. Many factors affect the chemical composition of the fruit as well as its mineral content, for example the temperature, the origin of the cultivar and the harvest period. In therapy, this plant is known for its cholesterol-lowering, antiproliferative, antidiarrheal effect.

Latitudinal distribution of freshwater sponge species across European Russia

This study provides original faunistic data on freshwater sponge dispersal across a huge territory of European Russia from north to south, highlighting the northern limits of thermophilic and north-adapted species. The holarctic species Ephydatia muelleri and, especially, Spongilla lacustris were predominant in northern areas, while the cosmopolitan Ephydatia fluviatilis and Eunapius fragilis were less prevalent. Moving to the south, E. fluviatilis took the lead. The distributional pattern of northern sponges aligns with literature data from North Europe, confirming the prevalence of the holarctic species in high latitudes. Tubella (=Trochospongilla) horrida, Eunapius carteri, and Radiospongilla cerebellata are considered to be thermophilic species that could not tolerate the conditions in northern regions. Notable findings include the extension of Eunapius carteri's known range and the first report of R. cerebellata within Russia, which is also the second record for Europe. Three potentially expected species were not found in the studied area, indicating regional rarity. We also provide molecular and morphological evidence for the synonymy of Spongilla arctica and Spongilla lacustris. Finally, we discuss the impacts of climate change and agricultural activities on northern and southern sponge habitats respectively.

Fatty acid content and profile of round sardinella (Sardinella aurita), an expanding thermophilic species in the NW Mediterranean

Over the past few decades, due to sea warming driven by global climate change, the habitat range of round sardinella (Sardinella aurita) has expanded into the north-western Mediterranean Sea. This study evaluates the fatty acid content and fatty acid profile of this small, warm-water pelagic fish caught in this area, specifically the northern Catalan coast. The findings provide important insights into the nutritional status of the species under changing environmental conditions. The study confirms that fatty acid content varies according to the individual specimen’s maturity stages (immature, pre-spawners, and spawners). Pre-spawners showed higher fat levels compared to spawners, whose lipids are allocated to their gonads to enhance the survival of their offspring. While a high content of omega-3 polyunsaturated fatty acids (n-3 PUFAs) was generally found at all stages of maturity, pre-spawners had higher levels of EPA but lower levels of DHA than immature individuals and spawners. Moreover, compared to small pelagic fish more typical of the temperate waters in the region (European anchovy, Engraulis encrasicolus, and European sardine, Sardina pilchardus), round sardinella generally have a higher level of PUFAs, especially DHA. Encouraging consumption of this warm water species could provide significant nutritional benefits while reducing fishing pressure on European sardine and European anchovy, whose populations are currently in a very poor state.

Efficiencies of Thermophilic Bacteria Species in Degrading Biodegradable Low-density Polyethylene Mixtures in Aquatic Ecosystems

The study examined the efficiencies of bacteria thermophiles responsible for the depolymerization of biodegradable Low-Density Polyethylene (LDPE) blends in two aquatic environments to suggest model bacteria species that could be used for reducing the accumulation of single-use LDPE in both marine and freshwater ecosystems. Each of the biodegradable LDPE, polyethylene, and cellulose was placed in respirometry jars filled with 500 mls of the freshwater and marine water respectively in a randomized design of 4 by 2 by 3 following the American Standard Testing and Materials (ASTM) procedure. To identify the bacteria species, bacterial isolation was done using pour plate and streak methods. The bacteria species were identified by morphological, biochemical, and molecular methods. The thermophilic bacteria species were confirmed by sequencing to be Bacillus cereus, Pseudomonas species among others. The results revealed that the bacteria isolates on LDPE were responsible for the biodegradation processes of the LDPE. This study concluded that Bacillus cereus and Pseudomonas species have the bioremediation potentials to break down single-use biodegradable Low-Density Polyethylene (LDPE) in aquatic environments within six (6) months.

Spatial distribution of the range-expanding species Seriola fasciata (Bloch, 1793) in Mediterranean Sea: From past to future

The Mediterranean Sea is a highly susceptible area to climate change, that facilitates the introduction of warm-affinity exotic species, contributing to the expansion of their biogeographical range. One such thermophilic species is the Atlantic fish Seriola fasciata, which has colonised this area over the past three decades. The present study analyzed its spatial distribution in the Mediterranean Sea to identify aggregation areas and dynamics over time, and the environmental predictors influencing its presence.The utilized statistical tools and the Species Distribution Model proved effective in identifying specific spatial and temporal distribution patterns, as well as discerning some environmental variables influencing the species presence, with distinctions recorded between juveniles and adults.S. fasciata was observed to be established in the central Mediterranean, with Fishing Aggregating Devices potentially influencing its presence, particularly of juveniles. Sea floor temperature and habitats emerged as the primary factors driving species distribution. An aggregation area in the Levant Sea, conducive mainly for the adults, was identified and is expected to intensify over time.These findings contribute valuable insights into a relatively understudied species and its presence in the Mediterranean Sea, where climate change is affecting marine biodiversity.

Urban dragonfly fauna of a Mediterranean city in south-western Europe: How suitable are artificial habitats for thermophilic species?

Urban dragonfly fauna of a Mediterranean city in south-western Europe: How suitable are artificial habitats for thermophilic species?

Exploring the Frozen Armory: Antiphage Defense Systems in Cold-Adapted Bacteria with a Focus on CRISPR-Cas Systems.

Our understanding of the antiphage defense system arsenal in bacteria is rapidly expanding, but little is known about its occurrence in cold-adapted bacteria. In this study, we aim to shed light on the prevalence and distribution of antiphage defense systems in cold-adapted bacteria, with a focus on CRISPR-Cas systems. Using bioinformatics tools, Prokaryotic Antiviral Defense LOCator (PADLOC) and CRISPRCasTyper, we mapped the presence and diversity of antiphage defense systems in 938 available genomes of cold-adapted bacteria from diverse habitats. We confirmed that CRISPR-Cas systems are less frequent in cold-adapted bacteria, compared to mesophilic and thermophilic species. In contrast, several antiphage defense systems, such as dXTPases and DRTs, appear to be more frequently compared to temperate bacteria. Additionally, our study provides Cas endonuclease candidates with a potential for further development into cold-active CRISPR-Cas genome editing tools. These candidates could have broad applications in research on cold-adapted organisms. Our study provides a first-time map of antiphage defense systems in cold-adapted bacteria and a detailed overview of CRISPR-Cas diversity.

Nest survival of Crested Lark (Galerida cristata) in intensively used habitats in Central Poland

Breeding success of birds depends on survival during two critical stages of the reproductive period: First, egg laying and incubation, and then nestling and fledgling. This essential element of avian life history mirrors an evolutionary adaptation of parents to existing environmental conditions. The main factors that determine nest survival involve weather, predation and sibling competition. Despite numerous studies documenting their impact on breeding success, only a few have analysed the issue with regard to ground-nesting birds and estimated their survival functions. Therefore, we decided to examine nest survival probability of the Crested Lark (Galerida cristata) in a population that occupies newly established roadside habitats in Central Poland. The analysis is based on 141 nests monitored between 2018 and 2022. We found that the mean survival probability of the whole nesting period was 0.376, and it was higher during the egg stage (0.836) than during the nestling period (0.392). The Cox proportional hazards model shows that nest survival in the nestling stage is mainly affected by the time of breeding and the distance from the road edge, and also by mean temperature of the whole nesting period. In other words, the probability of a brood failure in the nestling stage decreases as the breeding season advances, whereas it increases among nests located closer to the road edge. Furthermore, during the whole nesting period, nest failure decreases as the temperature rises. Our study suggests that the Crested Lark, being a multi-brood and thermophilic species inhabiting temperate regions, may benefit more if its nesting attempts begin later during the season when breeding conditions become more favourable. However, we also take into consideration a hypothesis that nesting in grassy habitats near road edges may prove to be an ecological trap, attracting high densities of nesting birds but leading to their low nest success.

Characterization of thermophilic bacteria from Ie Seum Hot Springs, Aceh Besar, Indonesia as producers of protease enzyme

Abstract. Sabaria E, Yasmin Y, Ismail YS, Bessania MA, Putri I, Fitri L. 2024. Characterization of thermophilic bacteria from Ie Seum Hot Springs, Aceh Besar, Indonesia as producers of protease enzyme. Biodiversitas 25: 1867-1874. Thermophilic bacteria are microorganisms that can survive in high-temperature environments exceeding 75°C. The Ie Seum Hot Springs in Aceh Besar, Indonesia are known to be a place where these thermophilic bacteria inhabit. In such extreme conditions, proteins and enzymes are often denatured, making these bacteria of interest due to their ability to adapt and produce enzymes such as proteases. Proteases are called proteolytic enzymes that can be applied both in the economic and medical fields. This study aimed to isolate and identify thermophilic bacteria species that have the highest potential for protease production in Ie Seum Hot Spring, Aceh Besar by analyzing the 16S rRNA gene and characterizing them using biochemical tests. Based on the result, seven thermophilic bacterial isolates, namely BT1, BT2, BT3, BT4, BT5, BT6, and BT7 were obtained, each showing different colony characteristics. The biochemical tests also revealed differences metabolic activity of each isolate. Of these isolates, BT4 exhibited the highest proteolytic index (4.65). Additionally, the 16S rRNA gene sequence analysis showed that the BT4 strain belongs to the genus Bacillus and has high similarities to Bacillus sp., B. licheniformis and B. sonorensis. These findings suggest that BT4 has significant potential as a source of thermophilic protease enzymes.

Structural Evolution of Bacterial Polyphosphate Degradation Enzyme for Phosphorus Cycling.

Living organisms ranging from bacteria to animals have developed their own ways to accumulate and store phosphate during evolution, in particular as the polyphosphate (polyP) granules in bacteria. Degradation of polyP into phosphate is involved in phosphorus cycling, and exopolyphosphatase (PPX) is the key enzyme for polyP degradation in bacteria. Thus, understanding the structure basis of PPX is crucial to reveal the polyP degradation mechanism. Here, it is found that PPX structure varies in the length of ɑ-helical interdomain linker (ɑ-linker) across various bacteria, which is negatively correlated with their enzymatic activity and thermostability - those with shorter ɑ-linkers demonstrate higher polyP degradation ability. Moreover, the artificial DrPPX mutants with shorter ɑ-linker tend to have more compact pockets for polyP binding and stronger subunit interactions, as well as higher enzymatic efficiency (kcat/Km) than that of DrPPX wild type. In Deinococcus-Thermus, the PPXs from thermophilic species possess a shorter ɑ-linker and retain their catalytic ability at high temperatures (70°C), which may facilitate the thermophilic species to utilize polyP in high-temperature environments. These findings provide insights into the interdomain linker length-dependent evolution of PPXs, which shed light on enzymatic adaption for phosphorus cycling during natural evolution and rational design of enzyme.

Role of Maternal Antibodies in the Protection of Broiler Chicks against Campylobacter Colonization in the First Weeks of Life.

Thermophilic Campylobacter species are the most common cause of bacterium-mediated diarrheal disease in humans globally. Poultry is considered the most important reservoir of human campylobacteriosis, but so far, no effective countermeasures are in place to prevent the bacterium from colonizing broiler flocks. This study investigated maternal antibodies' potential to offer protection against Campylobacter in broiler chicks via a field trial and an immunization trial. In the field trial, breeder flocks with high and low anti-Campylobacter antibody levels in the yolk were selected based on serological screening. Offspring were subsequently monitored for maternal antibodies and Campylobacter prevalence during early life. Although maternal antibodies declined rapidly in the serum of broilers, offspring from flocks with lower anti-Campylobacter antibody levels seemed to be more susceptible to colonization. In the immunization trial, breeders from a seropositive breeder flock were vaccinated with an experimental bacterin or subunit vaccine. Immunization increased antibody levels in the yolk and consequently in the offspring. Elevated maternal antibody levels were significantly associated with reduced Campylobacter susceptibility in broilers at 2 weeks old but not at 1 and 3 weeks old. Overall, the protective effect of maternal immunity should be cautiously considered in the context of Campylobacter control in broilers. Immunization of breeders may enhance resistance but is not a comprehensive solution.