Review

18 pages, 3624 KiB

Open AccessReview

Freshwater Sponges as a Neglected Reservoir of Bacterial Biodiversity

by Angelina Lo Giudice and Carmen Rizzo

Microorganisms 2024, 12(1), 25; https://doi.org/10.3390/microorganisms12010025 - 22 Dec 2023

Viewed by 817

Freshwater sponges (Spongillida: Demospongiae), including more than 240 described species, are globally distributed in continental waters (except for Antarctica), where they cover both natural and artificial surfaces. However, fragmentary studies have targeted their microbiome, making it difficult to test hypotheses about sponge-microbe specificity [...] Read more.

Freshwater sponges (Spongillida: Demospongiae), including more than 240 described species, are globally distributed in continental waters (except for Antarctica), where they cover both natural and artificial surfaces. However, fragmentary studies have targeted their microbiome, making it difficult to test hypotheses about sponge-microbe specificity and metabolic relationships, along with the environmental factors playing key roles in structuring the associated microbial communities. To date, particular attention has been paid to sponges (family Lubomirskiidae) that are endemic to Lake Baikal. Few other freshwater sponge species (e.g., Ephydatia spp., Eunapius spp., and Spongilla lacustris), from lakes and rivers spanning from Europe to South and North America, have been targeted for microbiological studies. Representatives of the phyla Proteobacteria, Bacteroidetes, and Actinobacteria largely predominated, and high differences were reported between the microbiome of freshwater and marine sponges. Several bacterial strains isolated from freshwater sponges can produce bioactive compounds, mainly showing antibiotic activities, with potential application in biotechnology. Understanding the roles played by sponge microbiomes in freshwater ecosystems is still in its infancy and has yet to be clarified to disentangle the ecological and evolutionary significance of these largely under-investigated microbial communities. This review was aimed at providing the main available information on the composition and biotechnological potential of prokaryotic communities associated with healthy freshwater sponges, as a neglected component of the global sponge microbiome, to stimulate researchers interested in the field. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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15 pages, 890 KiB

Open AccessReview

Interaction of Naturally Occurring Phytoplankton with the Biogeochemical Cycling of Mercury in Aquatic Environments and Its Effects on Global Hg Pollution and Public Health

by Zivan Gojkovic, Samuel Simansky, Alain Sanabria, Ivana Márová, Inés Garbayo and Carlos Vílchez

Microorganisms 2023, 11(8), 2034; https://doi.org/10.3390/microorganisms11082034 - 08 Aug 2023

Cited by 3 | Viewed by 1770

Abstract

The biogeochemical cycling of mercury in aquatic environments is a complex process driven by various factors, such as ambient temperature, seasonal variations, methylating bacteria activity, dissolved oxygen levels, and Hg interaction with dissolved organic matter (DOM). As a consequence, part of the Hg [...] Read more.

The biogeochemical cycling of mercury in aquatic environments is a complex process driven by various factors, such as ambient temperature, seasonal variations, methylating bacteria activity, dissolved oxygen levels, and Hg interaction with dissolved organic matter (DOM). As a consequence, part of the Hg contamination from anthropogenic activity that was buried in sediments is reinserted into water columns mainly in highly toxic organic Hg forms (methylmercury, dimethylmercury, etc.). This is especially prominent in the coastal shallow waters of industrial regions worldwide. The main entrance point of these highly toxic Hg forms in the aquatic food web is the naturally occurring phytoplankton. Hg availability, intake, effect on population size, cell toxicity, eventual biotransformation, and intracellular stability in phytoplankton are of the greatest importance for human health, having in mind that such Hg incorporated inside the phytoplankton cells due to biomagnification effects eventually ends up in aquatic wildlife, fish, seafood, and in the human diet. This review summarizes recent findings on the topic of organic Hg form interaction with natural phytoplankton and offers new insight into the matter with possible directions of future research for the prevention of Hg biomagnification in the scope of climate change and global pollution increase scenarios. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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18 pages, 1251 KiB

Open AccessReview

Microbial Risks Caused by Livestock Excrement: Current Research Status and Prospects

by Rashidin Abdugheni, Li Li, Zhen-Ni Yang, Yin Huang, Bao-Zhu Fang, Vyacheslav Shurigin, Osama Abdalla Abdelshafy Mohamad, Yong-Hong Liu and Wen-Jun Li

Microorganisms 2023, 11(8), 1897; https://doi.org/10.3390/microorganisms11081897 - 27 Jul 2023

Cited by 1 | Viewed by 1435

Abstract

Livestock excrement is a major pollutant yielded from husbandry and it has been constantly imported into various related environments. Livestock excrement comprises a variety of microorganisms including certain units with health risks and these microorganisms are transferred synchronically during the management and utilization [...] Read more.

Livestock excrement is a major pollutant yielded from husbandry and it has been constantly imported into various related environments. Livestock excrement comprises a variety of microorganisms including certain units with health risks and these microorganisms are transferred synchronically during the management and utilization processes of livestock excrement. The livestock excrement microbiome is extensively affecting the microbiome of humans and the relevant environments and it could be altered by related environmental factors as well. The zoonotic microorganisms, extremely zoonotic pathogens, and antibiotic-resistant microorganisms are posing threats to human health and environmental safety. In this review, we highlight the main feature of the microbiome of livestock excrement and elucidate the composition and structure of the repertoire of microbes, how these microbes transfer from different spots, and they then affect the microbiomes of related habitants as a whole. Overall, the environmental problems caused by the microbiome of livestock excrement and the potential risks it may cause are summarized from the microbial perspective and the strategies for prediction, prevention, and management are discussed so as to provide a reference for further studies regarding potential microbial risks of livestock excrement microbes. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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16 pages, 1568 KiB

Open AccessReview

Phylogenetic Revisit to a Review on Predatory Bacteria

by Saki Kamada, Ryoka Wakabayashi and Takeshi Naganuma

Microorganisms 2023, 11(7), 1673; https://doi.org/10.3390/microorganisms11071673 - 27 Jun 2023

Cited by 2 | Viewed by 2978

Abstract

Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, [...] Read more.

Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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17 pages, 2017 KiB

Open AccessReview

Biological Degradation of Plastics and Microplastics: A Recent Perspective on Associated Mechanisms and Influencing Factors

by Zeming Cai, Minqian Li, Ziying Zhu, Xiaocui Wang, Yuanyin Huang, Tianmu Li, Han Gong and Muting Yan

Microorganisms 2023, 11(7), 1661; https://doi.org/10.3390/microorganisms11071661 - 26 Jun 2023

Cited by 21 | Viewed by 14328

Abstract

Plastic and microplastic pollution has caused a great deal of ecological problems because of its persistence and potential adverse effects on human health. The degradation of plastics through biological processes is of great significance for ecological health, therefore, the feasibility of plastic degradation [...] Read more.

Plastic and microplastic pollution has caused a great deal of ecological problems because of its persistence and potential adverse effects on human health. The degradation of plastics through biological processes is of great significance for ecological health, therefore, the feasibility of plastic degradation by microorganisms has attracted a lot of attention. This study comprises a preliminary discussion on the biodegradation mechanism and the advantages and roles of different bacterial enzymes, such as PET hydrolase and PCL-cutinase, in the degradation of different polymers, such as PET and PCL, respectively. With a particular focus on their modes of action and potential enzymatic mechanisms, this review sums up studies on the biological degradation of plastics and microplastics related to mechanisms and influencing factors, along with their enzymes in enhancing the degradation of synthetic plastics in the process. In addition, biodegradation of plastic is also affected by plastic additives and plasticizers. Plasticizers and additives in the composition of plastics can cause harmful impacts. To further improve the degradation efficiency of polymers, various pretreatments to improve the efficiency of biodegradation, which can cause a significant reduction in toxic plastic pollution, were also preliminarily discussed here. The existing research and data show a large number of microorganisms involved in plastic biodegradation, though their specific mechanisms have not been thoroughly explored yet. Therefore, there is a significant potential for employing various bacterial strains for efficient degradation of plastics to improve human health and safety. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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21 pages, 921 KiB

Open AccessReview

Microbial Growth under Limiting Conditions-Future Perspectives

by Juan M. Gonzalez and Beatriz Aranda

Microorganisms 2023, 11(7), 1641; https://doi.org/10.3390/microorganisms11071641 - 23 Jun 2023

Cited by 9 | Viewed by 7439

Abstract

Microorganisms rule the functioning of our planet and each one of the individual macroscopic living creature. Nevertheless, microbial activity and growth status have always been challenging tasks to determine both in situ and in vivo. Microbial activity is generally related to growth, and [...] Read more.

Microorganisms rule the functioning of our planet and each one of the individual macroscopic living creature. Nevertheless, microbial activity and growth status have always been challenging tasks to determine both in situ and in vivo. Microbial activity is generally related to growth, and the growth rate is a result of the availability of nutrients under adequate or adverse conditions faced by microbial cells in a changing environment. Most studies on microorganisms have been carried out under optimum or near-optimum growth conditions, but scarce information is available about microorganisms at slow-growing states (i.e., near-zero growth and maintenance metabolism). This study aims to better understand microorganisms under growth-limiting conditions. This is expected to provide new perspectives on the functions and relevance of the microbial world. This is because (i) microorganisms in nature frequently face conditions of severe growth limitation, (ii) microorganisms activate singular pathways (mostly genes remaining to be functionally annotated), resulting in a broad range of secondary metabolites, and (iii) the response of microorganisms to slow-growth conditions remains to be understood, including persistence strategies, gene expression, and cell differentiation both within clonal populations and due to the complexity of the environment. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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19 pages, 1036 KiB

Open AccessReview

The Mystery of Piezophiles: Understudied Microorganisms from the Deep, Dark Subsurface

by Gabrielle Scheffer and Lisa M. Gieg

Microorganisms 2023, 11(7), 1629; https://doi.org/10.3390/microorganisms11071629 - 22 Jun 2023

Cited by 1 | Viewed by 2290

Abstract

Microorganisms that can withstand high pressure within an environment are termed piezophiles. These organisms are considered extremophiles and inhabit the deep marine or terrestrial subsurface. Because these microorganisms are not easily accessed and require expensive sampling methods and laboratory instruments, advancements in this [...] Read more.

Microorganisms that can withstand high pressure within an environment are termed piezophiles. These organisms are considered extremophiles and inhabit the deep marine or terrestrial subsurface. Because these microorganisms are not easily accessed and require expensive sampling methods and laboratory instruments, advancements in this field have been limited compared to other extremophiles. This review summarizes the current knowledge on piezophiles, notably the cellular and physiological adaptations that such microorganisms possess to withstand and grow in high-pressure environments. Based on existing studies, organisms from both the deep marine and terrestrial subsurface show similar adaptations to high pressure, including increased motility, an increase of unsaturated bonds within the cell membrane lipids, upregulation of heat shock proteins, and differential gene-regulation systems. Notably, more adaptations have been identified within the deep marine subsurface organisms due to the relative paucity of studies performed on deep terrestrial subsurface environments. Nevertheless, similar adaptations have been found within piezophiles from both systems, and therefore the microbial biogeography concepts used to assess microbial dispersal and explore if similar organisms can be found throughout deep terrestrial environments are also briefly discussed. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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17 pages, 2503 KiB

Open AccessReview

Cellular Damage of Bacteria Attached to Senescent Phytoplankton Cells as a Result of the Transfer of Photochemically Produced Singlet Oxygen: A Review

by Jean-François Rontani and Patricia Bonin

Microorganisms 2023, 11(6), 1565; https://doi.org/10.3390/microorganisms11061565 - 13 Jun 2023

Viewed by 1107

Abstract

Several studies set out to explain the presence of high proportions of photooxidation products of cis-vaccenic acid (generally considered to be of bacterial origin) in marine environments. These studies show that these oxidation products result from the transfer of singlet oxygen from senescent [...] Read more.

Several studies set out to explain the presence of high proportions of photooxidation products of cis-vaccenic acid (generally considered to be of bacterial origin) in marine environments. These studies show that these oxidation products result from the transfer of singlet oxygen from senescent phytoplankton cells to the bacteria attached to them in response to irradiation by sunlight. This paper summarizes and reviews the key findings of these studies, i.e., the demonstration of the process at work and the effect of different parameters (intensity of solar irradiance, presence of bacterial carotenoids, and presence of polar matrices such as silica, carbonate, and exopolymeric substances around phytoplankton cells) on this transfer. A large part of this review looks at how this type of alteration of bacteria can affect the preservation of algal material in the marine environment, especially in polar regions where conditions drive increased transfer of singlet oxygen from sympagic algae to bacteria. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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31 pages, 2816 KiB

Open AccessReview

Exopolysaccharides Producing Bacteria: A Review

by Alexander I. Netrusov, Elena V. Liyaskina, Irina V. Kurgaeva, Alexandra U. Liyaskina, Guang Yang and Viktor V. Revin

Microorganisms 2023, 11(6), 1541; https://doi.org/10.3390/microorganisms11061541 - 09 Jun 2023

Cited by 11 | Viewed by 5842

Abstract

Bacterial exopolysaccharides (EPS) are essential natural biopolymers used in different areas including biomedicine, food, cosmetic, petroleum, and pharmaceuticals and also in environmental remediation. The interest in them is primarily due to their unique structure and properties such as biocompatibility, biodegradability, higher purity, hydrophilic [...] Read more.

Bacterial exopolysaccharides (EPS) are essential natural biopolymers used in different areas including biomedicine, food, cosmetic, petroleum, and pharmaceuticals and also in environmental remediation. The interest in them is primarily due to their unique structure and properties such as biocompatibility, biodegradability, higher purity, hydrophilic nature, anti-inflammatory, antioxidant, anti-cancer, antibacterial, and immune-modulating and prebiotic activities. The present review summarizes the current research progress on bacterial EPSs including their properties, biological functions, and promising applications in the various fields of science, industry, medicine, and technology, as well as characteristics and the isolation sources of EPSs-producing bacterial strains. This review provides an overview of the latest advances in the study of such important industrial exopolysaccharides as xanthan, bacterial cellulose, and levan. Finally, current study limitations and future directions are discussed. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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15 pages, 658 KiB

Open AccessReview

The Microbiome of Things: Appliances, Machines, and Devices Hosting Artificial Niche-Adapted Microbial Communities

by Leila Satari, Alba Iglesias and Manuel Porcar

Microorganisms 2023, 11(6), 1507; https://doi.org/10.3390/microorganisms11061507 - 06 Jun 2023

Cited by 1 | Viewed by 2593

Abstract

As it is the case with natural substrates, artificial surfaces of man-made devices are home to a myriad of microbial species. Artificial products are not necessarily characterized by human-associated microbiomes; instead, they can present original microbial populations shaped by specific environmental—often extreme—selection pressures. [...] Read more.

As it is the case with natural substrates, artificial surfaces of man-made devices are home to a myriad of microbial species. Artificial products are not necessarily characterized by human-associated microbiomes; instead, they can present original microbial populations shaped by specific environmental—often extreme—selection pressures. This review provides a detailed insight into the microbial ecology of a range of artificial devices, machines, and appliances, which we argue are specific microbial niches that do not necessarily fit in the “build environment” microbiome definition. Instead, we propose here the Microbiome of Things (MoT) concept analogous to the Internet of Things (IoT) because we believe it may be useful to shed light on human-made, but not necessarily human-related, unexplored microbial niches. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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14 pages, 993 KiB

Open AccessReview

Cold Sulfur Springs—Neglected Niche for Autotrophic Sulfur-Oxidizing Bacteria

by Lea Nosalova, Maria Piknova, Mariana Kolesarova and Peter Pristas

Microorganisms 2023, 11(6), 1436; https://doi.org/10.3390/microorganisms11061436 - 29 May 2023

Cited by 3 | Viewed by 1540

Abstract

Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. [...] Read more.

Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments. Although they have been of interest to microbiologists for more than 150 years, meso- and psychrophilic chemolithoautotrophic sulfur-oxidizing microbiota are less studied compared to the microbiota of hot springs. Several recent studies suggested that cold sulfur waters harbor unique, yet not described, bacterial taxa. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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24 pages, 4528 KiB

Open AccessReview

An Overview of Phytophthora Species on Woody Plants in Sweden and Other Nordic Countries

by Iryna Matsiakh and Audrius Menkis

Microorganisms 2023, 11(5), 1309; https://doi.org/10.3390/microorganisms11051309 - 17 May 2023

Cited by 1 | Viewed by 2732

Abstract

The genus Phytophthora, with 326 species in 12 phylogenetic clades currently known, includes many economically important pathogens of woody plants. Different Phytophthora species often possess a hemibiotrophic or necrotrophic lifestyle, have either a broad or narrow host range, can cause a variety [...] Read more.

The genus Phytophthora, with 326 species in 12 phylogenetic clades currently known, includes many economically important pathogens of woody plants. Different Phytophthora species often possess a hemibiotrophic or necrotrophic lifestyle, have either a broad or narrow host range, can cause a variety of disease symptoms (root rot, damping-off, bleeding stem cankers, or blight of foliage), and occur in different growing environments (nurseries, urban and agricultural areas, or forests). Here, we summarize the available knowledge on the occurrence, host range, symptoms of damage, and aggressiveness of different Phytophthora species associated with woody plants in Nordic countries with a special emphasis on Sweden. We evaluate the potential risks of Phytophthora species to different woody plants in this geographical area and emphasize the increasing threats associated with continued introduction of invasive Phytophthora species. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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16 pages, 6283 KiB

Open AccessReview

Halobacteria-Based Biofertilizers: A Promising Alternative for Enhancing Soil Fertility and Crop Productivity under Biotic and Abiotic Stresses—A Review

by Fatma Masmoudi, Mohammed Alsafran, Hareb AL Jabri, Hoda Hosseini, Mohammed Trigui, Sami Sayadi, Slim Tounsi and Imen Saadaoui

Microorganisms 2023, 11(5), 1248; https://doi.org/10.3390/microorganisms11051248 - 09 May 2023

Cited by 4 | Viewed by 2208

Abstract

Abiotic and biotic stresses such as salt stress and fungal infections significantly affect plant growth and productivity, leading to reduced crop yield. Traditional methods of managing stress factors, such as developing resistant varieties, chemical fertilizers, and pesticides, have shown limited success in the [...] Read more.

Abiotic and biotic stresses such as salt stress and fungal infections significantly affect plant growth and productivity, leading to reduced crop yield. Traditional methods of managing stress factors, such as developing resistant varieties, chemical fertilizers, and pesticides, have shown limited success in the presence of combined biotic and abiotic stress factors. Halotolerant bacteria found in saline environments have potential as plant promoters under stressful conditions. These microorganisms produce bioactive molecules and plant growth regulators, making them a promising agent for enhancing soil fertility, improving plant resistance to adversities, and increasing crop production. This review highlights the capability of plant-growth-promoting halobacteria (PGPH) to stimulate plant growth in non-saline conditions, strengthen plant tolerance and resistance to biotic and abiotic stressors, and sustain soil fertility. The major attempted points are: (i) the various abiotic and biotic challenges that limit agriculture sustainability and food safety, (ii) the mechanisms employed by PGPH to promote plant tolerance and resistance to both biotic and abiotic stressors, (iii) the important role played by PGPH in the recovery and remediation of agricultural affected soils, and (iv) the concerns and limitations of using PGHB as an innovative approach to boost crop production and food security. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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22 pages, 1628 KiB

Open AccessReview

Recent Progress of Reclassification of the Genus Streptomyces

by Hisayuki Komaki

Microorganisms 2023, 11(4), 831; https://doi.org/10.3390/microorganisms11040831 - 24 Mar 2023

Cited by 10 | Viewed by 3023

Abstract

The genus Streptomyces is a representative group of actinomycetes and one of the largest taxa in bacteria, including approximately 700 species with validly published names. Since the classification was mainly based on phenotypic characteristics in old days, many members needed to be reclassified [...] Read more.

The genus Streptomyces is a representative group of actinomycetes and one of the largest taxa in bacteria, including approximately 700 species with validly published names. Since the classification was mainly based on phenotypic characteristics in old days, many members needed to be reclassified according to recent molecular-based taxonomies. Recent developments of molecular-based analysis methods and availability of whole genome sequences of type strains enables researchers to reclassify these phylogenetically complex members on a large scale. This review introduces reclassifications of the genus Streptomyces reported in the past decade. Appropriately 34 Streptomyces species were transferred to the other genera, such as Kitasatospora, Streptacidiphilus, Actinoalloteichus and recently proposed new genera. As a result of reclassifications of 14 subspecies, the genus Streptomyces includes only four subspecies at present in practice. A total of 63 species were reclassified as later heterotypic synonyms of previously recognized species in 24 published reports. As strong relationships between species and the secondary metabolite-biosynthetic gene clusters become clarified, appropriate classifications of this genus will not only contribute to systematics, but also provide significant information when searching for useful bioactive substances. Full article

(This article belongs to the Special Issue Latest Review Papers in Environmental Microbiology 2023)

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