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Articles Corrected proof have been peer-reviewed and accepted, which are not yet assigned to volumes/issues, but are citable by Digital Object Identifier (DOI).
Review
From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes
Nimaichand Salam, Wen-Dong Xian, Mipeshwaree Devi Asem, Min Xiao, Wen-Jun Li
, Available online  , doi: 10.1007/s42995-020-00064-w
Abstract(22) HTML PDF Springerlink
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Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.
Planktonic microbial eukaryotes in polar surface waters:recent advances in high-throughput sequencing
Qian Liu, Qiannan Zhao, Andrew McMinn, Eun Jin Yang, Yong Jiang
, Available online  , doi: 10.1007/s42995-020-00062-y
Abstract(90) HTML PDF Springerlink
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Marine microbial eukaryotes are important primary producers and play critical roles in key biogeochemical cycles. Recent advances in sequencing technology have focused attention on the extent of microbial biodiversity, revealing a huge, previously underestimated phylogenetic diversity with many new lineages. This technology has now become the most important tool to understand the ecological significance of this huge and novel diversity in polar oceans. In particular, high-throughput sequencing technologies have been successfully applied to enumerate and compare marine microbial diversity in polar environments. Here, a brief overview of polar microbial eukaryote diversity, as revealed by in-situ surveys of the high-throughput sequencing on 18S rRNA gene, is presented. Using these 'omic' approaches, further attention still needs to be focused on differences between specific locations and/or entire polar oceans and on bipolar comparisons of diversity and distribution.
Proteases from the marine bacteria in the genus Pseudoalteromonas: diversity, characteristics, ecological roles, and application potentials
Xiu-Lan Chen, Yan Wang, Peng Wang, Yu-Zhong Zhang
, Available online  , doi: 10.1007/s42995-020-00058-8
Abstract(47) HTML PDF Springerlink
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Bacterial strains of the genus Pseudoalteromonas, which includes 48 species, are widely distributed in various ocean environments. Many strains are often abundant and the highest protease producer among marine culturable protease-secreting bacteria, suggesting their important role in marine organic nitrogen degradation and cycling. The extracellular proteases of Pseudoalteromonas are diverse, including serine proteases, metalloproteases, and cystine proteases. Pseudoalteromonas proteases have unique properties, such as cold adaptation, salt tolerance, distinct substrate specificity, and catalytic mechanism. They play important ecological roles in marine organic nitrogen degradation and in the interactions of Pseudoalteromonas with other organisms. Some Pseudoalteromonas proteases have shown promising application potentials in bioactive peptide preparation and meat processing. In this review, advances in our knowledge of Pseudoalteromonas proteases are introduced, with a focus on diversity, characters, ecological significance, and application potentials.
Roles of dietary taurine in fish nutrition
W. W. H. A. Sampath, R. M. D. S. Rathnayake, Mengxi Yang, Wenbing Zhang, Kangsen Mai
, Available online  , doi: 10.1007/s42995-020-00051-1
Abstract(166) HTML PDF Springerlink
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Taurine is a conditionally essential amino acid in fish nutrition. The present study addressed the practical application of examining published data on fish nutrition over the past 20 years, emphasizing the topic of taurine by using computational tools and their applications. According to the published articles, an increased linear growth of research occurred, with Japanese flounder being the most examined fish species. Dietary taurine supplementation has several beneficial effects in fish nutrition, such as survival, growth, feed utilization, protein and energy retention, intermediate metabolism, anti-oxidation, anti-stress, disease resistance, muscle texture and reproductive performance. Also, there are negative effects in some species. Dietary taurine exerted effects on several gene expressions and enzyme activities; these are important in taurine metabolism in fish. These genes and enzymes included taurine transporter (TauT), cysteine dioxygenase (CDO), cysteamine dioxygenase (ADO), cysteine sulfonate decarboxylase (CSD) and pretrypsinogen (Ptry). Plant protein-based diets with taurine supplementation are recommended because of the absence of taurine in plant protein.
Environmental perspectives of microplastic pollution in the aquatic environment: a review
Manzoor Ahmad, Jia-Ling Li, Pan-Deng Wang, Wael N. Hozzein, Wen-Jun Li
, Available online  , doi: 10.1007/s42995-020-00056-w
Abstract(73) HTML PDF Springerlink
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Microplastics are a highly concerning pollutant that have gained attention from the scientific community and other regulatory authorities due to their potential risks to organisms and ecosystems. Microplastics are widespread in both terrestrial and aquatic ecosystems and can be found even in Antarctica and deep-sea sediments. The ability to survive for long periods in the environment and their aptitude of inter- and intra-environmental translocation can prompt poor environmental outcomes. The adsorption of heavy metals and other toxic persistent organic pollutants is a further cause for concern. Furthermore,microplastics enable the development of a distinct microbial niche within an ecosystem,which could potentially impair ecosystem function by promoting the growth of selective microbial communities. The acquisition of metal-resistant,antibiotic-resistant genes,and the enrichment of antibiotic-resistant bacteria on microplastic surfaces have recently been reported. Moreover,some studies have also reported the colonization of pathogenic bacterial strains such as Vibrio spp. on microplastic surfaces. This review aims to address the sources of microplastic pollution in the freshwater and marine environments and to discuss their potential functions in the environment.
Strategies for culturing active/dormant marine microbes
Da-Shuai Mu, Yang Ouyang, Guan-Jun Chen, Zong-Jun Du
, Available online  , doi: 10.1007/s42995-020-00053-z
Abstract(91) HTML PDF Springerlink
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Microorganisms are ubiquitous in the ocean environment and they play key roles in marine ecosystem function and service. However,many of their functions and phenotypes remain unknown because indigenous marine bacteria are mostly difficult to culture. Although many novel techniques have brought previously uncultured microbes into laboratory culture,there are still many most-wanted or key players that need to be cultured from marine environments. This review discusses possible reasons for 'unculturable microbes' and categorizes uncultured bacteria into three groups: dominant active bacteria,rare active bacteria,and dormant bacteria. This review also summarizes advances in cultivation techniques for culturing each group of unculturable bacteria. Simulating the natural environment is an effective strategy for isolating dominant active bacteria,whereas culturomics and enrichment culture methods are proposed for isolating rare active bacteria. For dormant bacteria,resuscitation culture is an appropriate strategy. Furthermore,the review provides a list of the most-wanted bacteria and proposes potential strategies for culturing these bacteria in marine environments. The review provides new insight into the development of strategies for the cultivation of specific groups of uncultured bacteria and therefore paves the way for the detection of novel microbes and their functions in marine ecosystems.
Applications of chitosan-based biomaterials: a focus on dependent antimicrobial properties
Zhenwei Deng, Ting Wang, Xiguang Chen, Ya Liu
, Available online  , doi: 10.1007/s42995-020-00044-0
Abstract(619) HTML PDF Springerlink
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Marine-derived chitosan has been widely examined for its use in developing biomedical materials. Not only is it non-toxic, biocompatible, and degradable, it has also shown unique antimicrobial properties. The antimicrobial properties of chitosan are restricted by neutral and physiological conditions because it is insoluble in water and its pKa values is 6.5. One solution to this problem is to graft chemically modified groups onto the backbone of chitosan. The aim of this paper is to review the mode of antimicrobial action of chitosan and chitosan derivatives. Using chitosan alone may not meet the demands of various applications. However, the introduction of additional polymers and antimicrobial agents is commonly used to enhance the antimicrobial potential of chitosan-based biomaterials. Chitosan-based composite biomaterials have been developed that allow diversified formulations to broaden applications, including nanoparticles, hydrogels, films, sponges, fibers, or even microspheres. These along with recent advances on chitosan-based composite biomaterials used for wound healing, food packaging, textile sector, 3D printing and dental materials, were reviewed in detail.
Viable but nonculturable bacteria and their resuscitation: implications for cultivating uncultured marine microorganisms
Xiao-Hua Zhang, Waqar Ahmad, Xiao-Yu Zhu, Jixiang Chen, Brian Austin
, Available online  , doi: 10.1007/s42995-020-00041-3
Abstract(169) HTML PDF Springerlink
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Culturing has been the cornerstone of microbiology since Robert Koch first successfully cultured bacteria in the late nineteenth century. However, even today, the majority of microorganisms in the marine environment remain uncultivated. There are various explanations for the inability to culture bacteria in the laboratory, including lack of essential nutrients, osmotic support or incubation conditions, low growth rate, development of micro-colonies, and the presence of senescent or viable but nonculturable (VBNC) cells. In the marine environment, many bacteria have been associated with dormancy, as typified by the VBNC state. VBNC refers to a state where bacteria are metabolically active, but are no longer culturable on routine growth media. It is apparently a unique survival strategy that has been adopted by many microorganisms in response to harsh environmental conditions and the bacterial cells in the VBNC state may regain culturability under favorable conditions. The resuscitation of VBNC cells may well be an important way to cultivate the otherwise uncultured microorganisms in marine environments. Many resuscitation stimuli that promote the restoration of culturability have so far been identified; these include sodium pyruvate, quorum sensing autoinducers, resuscitation-promoting factors Rpfs and YeaZ, and catalase. In this review, we focus on the issues associated with bacterial culturability, the diversity of bacteria entering the VBNC state, mechanisms of induction into the VBNC state, resuscitation factors of VBNC cells and implications of VBNC resuscitation stimuli for cultivating these otherwise uncultured microorganisms. Bringing important microorganisms into culture is still important in the era of high-throughput sequencing as their ecological functions in the marine environment can often only be known through isolation and cultivation.
Research Paper
Acetylcholinesterase inhibitors and antioxidants mining from marine fungi: bioassays, bioactivity coupled LC–MS/MS analyses and molecular networking
Yingying Nie, Wencong Yang, Yayue Liu, Jingming Yang, Xiaoling Lei, William H. Gerwick, Yi Zhang
, Available online  , doi: 10.1007/s42995-020-00065-9
Abstract(15) HTML PDF Springerlink
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Marine fungi are potentially important resources for bioactive lead compounds for discovering new drugs for diseases such as Alzheimer's disease. In this paper, the combined bioassay model of acetylcholinesterase (AChE) inhibition, 1, 1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging, and Artemia larval lethality was used to evaluate the activity and toxicity of 35 marine fungal strains from seas around China. Their bioactive constituents were revealed by thin layer chromatography (TLC) autography, bioactivity coupled LC–MS/MS and Global Natural Products Social Molecular Networking (GNPS). The results show that the extracts of five strains exhibited higher AChE inhibition ratios than the positive control compound, 'tacrine', for which the ratio was 89.8% at 200 μg/ml. Six strains displayed both AChE inhibition (inhibition ratios>20% at 200 μg/ml) and DPPH scavenging activity (scavenging ratios>30% at 200 μg/ml) together with low Artemia larval toxicity (lethal rates<12%). TLC autography showed that the fractioned extracts of four strains contained highly diverse and different bioactive constituents, including strains Talaromyces sp. C21-1, Aspergillus terreus C23-3, Trichoderma harzianum DLEN2008005, and Penicillium corylophilum TBG1-17. From the most potent sample F-11-1-b (derived from Aspergillus terreus C23-3), five AChE inhibitors and seven antioxidants were recognized as bioactive molecules by AChE coupled ultrafiltration followed by LC–MS/MS, and LC–MS/MS coupled with DPPH incubation. Furthermore, with the aid of GNPS, the AChE inhibitors were plausibly annotated as territrem analogues including territrems A–C/D, arisugacin A and an unknown compound 4, and the seven antioxidants were assigned as butyrolactone Ι, aspernolide E, a phenolic derivative and possibly unknown compounds 810 and 12.
Metabolic diversification of anaerobic methanotrophic archaea in a deep-sea cold seep
Wen-Li Li, Yu-Zhi Wu, Guo-wei Zhou, Hui Huang, Yong Wang
, Available online  , doi: 10.1007/s42995-020-00057-9
Abstract(104) HTML PDF Springerlink
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Anaerobic methanotrophic archaea (ANME) can assimilate methane and govern the greenhouse effect of deep-sea cold seeps. In this study, a total of 13 ANME draft genomes representing five ANME types (ANME-1a, ANME-1b, ANME-2a, ANME-2b and ANME-2c), in size between 0.8 and 1.8 Mbp, were obtained from the Jiaolong cold seep in the South China Sea. The small metagenome-assembled genomes (MAGs) contained all the essential pathways for methane oxidization and carbon dioxide fixation. All genes related to nitrate and sulfate reduction were absent from the MAGs, indicating their syntrophic dependence on partner organisms. Aside from acetate secretion and sugar storage, propanoate synthesis pathway, as an alternative novel carbon flow, was identified in all the MAGs and transcriptionally active. Regarding type-specific features of the MAGs, the genes encoding archaellum and bacteria-derived chemotaxis were specific to ANME-2, perhaps for fitness under fluctuation of methane and sulfate concentration flux. Our genomic and transcriptomic results strongly suggested that ANME could carry out simple carbon metabolism from C1 assimilation to C3 biosynthesis in the SCS cold seep, which casts light on a novel approach for synthetic biology.
Identification, expression analysis, and functional characterization of ghrelin and its receptors in spotted sea bass (Lateolabrax maculatus)
Peng Yu, Yangyang Zhou, Xin Qi, Hongying Fan, Kaiqiang Zhang, Xiaoyan Zhang, Yun Li, Haishen Wen
, Available online  , doi: 10.1007/s42995-020-00055-x
Abstract(96) HTML PDF Springerlink
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Ghrelin (Ghrl), an appetite-inducing peptide hormone secreted by the stomach, is the endogenous ligand for the growth hormone secretagogue receptor (Ghs-r). In this study, we identified the preproghrelin gene and its receptors in spotted sea bass (Lateolabrax maculatus). The ghrl gene consisted of an open reading frame (ORF) of 324 nucleotides encoding 107 amino acids, and the premature protein contained a 20-amino-acid mature peptide. Through a syntenic analysis, we also validated the annotation of growth hormone secretagogue receptor 1a (ghs-r1a) and growth hormone secretagogue receptor 1a-like (ghs-r1a-like), which contained seven-transmembrane structures, in spotted sea bass. The ORF of ghs-r1a consisted of 1152 bp that encoded a 383-amino-acid protein, and ghs-r1a-like contained an ORF of 2631 bp and produced a protein with 876 amino acids. A phylogenetic analysis showed that spotted sea bass ghrl and its receptors clustered with those of other fishes and were more distantly related to those of other vertebrates. In situ hybridization revealed that ghrl was highly expressed in the stomach and localized in the mucosa and submucosa. The expression of these genes varied during short-term starvation in a time-dependent manner. In vitro studies showed that after incubation with Ghrl for 3 h enhanced the expression of motilin (mln), gastrin (gas) and cholecystokinin (cck), but this effect vanished after 6 h of incubation. In summary, Ghrl and its receptors might play important roles in the regulation of food intake in spotted sea bass.
Grazing by microzooplankton and copepods on the microbial food web in spring in the southern Yellow Sea, China
Yuan Zhao, Yi Dong, Haibo Li, Shiquan Lin, Lingfeng Huang, Tian Xiao, Gerald Gregori, Li Zhao, Wuchang Zhang
, Available online  , doi: 10.1007/s42995-020-00047-x
Abstract(103) HTML PDF Springerlink
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Assessment of microzooplankton and copepods grazing pressure on picoplankton is a key requirement for resolving the microbial food web efficiency. Although microzooplankton grazing on picoplankton has been extensively studied, the impact of microzooplankton on different groups of picoplankton, i.e., heterotrophic bacteria, Synechococcus and picoeukaryotes have rarely been compared. Furthermore, in the very few existing studies there is no consistent evidence of an enhancing or restraining effect of copepods on picoplankton. More studies are needed to improve our understanding of the influence of microzooplankton and copepod on picoplankton. Dilution incubations and copepod addition incubations were performed during a cruise to the southern Yellow Sea on May 16–29, 2007. The bulk grazing of microzooplankton and the calanoid copepod Calanus sinicus on phytoplankton, flagellates and picoplankton was estimated. Stations were divided into either eutrophic or oligotrophic according to the nutrient and biological parameters. Picoplankton comprised a large part of the diet of microzooplankton in the central oligotrophic area, while phytoplankton was the main food of microzooplankton in the coastal eutrophic area. In the central oligotrophic area, microzooplankton preferred grazing on Synechococcus. After copepod addition, ciliate abundance decreased while Synechococcus abundance increased (382%, 64% and 64% at three experimental stations, respectively), indicating strong grazing pressure of microzooplankton on Synechococcus. Our results suggest that Synechococcus might be an essential carbon source the planktonic food web in the oligotrophic waters of southern Yellow Sea.
The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria
Jiao Pan, Emily Williams, Way Sung, Michael Lynch, Hongan Long
, Available online  , doi: 10.1007/s42995-020-00060-0
Abstract(87) HTML PDF Springerlink
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Mutation is a primary source of genetic variation that is used to power evolution. Many studies, however, have shown that most mutations are deleterious and, as a result, extremely low mutation rates might be beneficial for survival. Using a mutation accumulation experiment, an unbiased method for mutation study, we found an extremely low base-substitution mutation rate of 5.94×10-11 per nucleotide site per cell division (95% Poisson confidence intervals: 4.65×10-11, 7.48×10-11) and indel mutation rate of 8.25×10-12 per site per cell division (95% confidence intervals: 3.96×10-12, 1.52×10-11) in the bacterium Photorhabdus luminescens ATCC29999. The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction. It has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the effective population size (drift-barrier hypothesis) and we found that the effective population size of this bacterium is significantly greater than most other bacteria. This finding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fidelity can evolve within organisms that maintain large effective population sizes.
Optimal amounts of coconut oil in diets improve the growth, antioxidant capacity and lipid metabolism of large yellow croaker (Larimichthys crocea)
Tao Ding, Ning Xu, Yongtao Liu, Xueshan Li, Xiaojun Xiang, Dan Xu, Chuanwei Yao, Qiangde Liu, Zhaoyang Yin, Kangsen Mai, Qinghui Ai
, Available online  , doi: 10.1007/s42995-020-00045-z
Abstract(195) HTML PDF Springerlink
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The purpose of this study was to investigate the effect of different dietary coconut oil (CO) levels on growth, antioxidant capacity and lipid metabolism of juvenile large yellow croaker (Larimichthys crocea). Five iso-nitrogen (45% crude protein) and iso-lipid (13% crude lipid) experimental diets were prepared by replacing 0% (the control), 25%, 50%, 75% and 100% fish oil with coconut oil. The results showed that dietary CO had no significant effect on survival rate (SR, P > 0.05). However, the specific growth rate was increased significantly when compared with the control group when fish were fed the diet with 50% CO (P < 0.05). The saturated fatty acids were increased significantly with increasing dietary CO in the liver and muscle, whereas the content of n-3 PUFA was decreased significantly (P < 0.05). The highest activities of glutathione peroxidase and superoxide dismutase in the liver were recorded in fish-fed diet with 50% CO; conversely, the content of malondialdehyde was significantly decreased (P < 0.05). The mRNA expression of peroxisome proliferator-activated receptor α, carnitine palmitoyl transferase 1 and acyl-CoA oxidase reached the highest levels in fish-fed diet with 50% CO. To some extent, this indicated that the rapid oxidation reaction of fatty acids to provide energy may be the reason for the rapid growth of large yellow croaker. In conclusion, fish-fed diet with 50% CO increased the growth rate and antioxidant capacity. Therefore, the optimal replacement level of CO to FO in the diet should be 50%.
Morphology, taxonomy and molecular phylogeny of three marine peritrich ciliates, including two new species: Zoothamnium apoarbuscula n. sp. and Z. apohentscheli n. sp. (Protozoa, Ciliophora, Peritrichia)
Tong Wu, Yuqing Li, Borong Lu, Zhuo Shen, Weibo Song, Alan Warren
, Available online  , doi: 10.1007/s42995-020-00046-y
Abstract(716) HTML PDF Springerlink
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Zoothamnium is a speciose genus, most species of which have incomplete morphological data based on modern criteria. In the present study, the morphology of three species of Zoothamnium, i.e., Z. apoarbuscula n. sp., Z. apohentscheli n. sp., and Z. alternans, collected in Qingdao, China, was revealed using living observation and silver staining. In addition, the SSU rDNA of each species was sequenced for phylogenetic analyses. Zoothamnium apoarbuscula n. sp. is characterized by its umbellate colony which is up to 900 μm high, dichotomously branched stalk, differentiation of zooids, and infundibular polykinety 3 comprising three equal-length ciliary rows. Zoothamnium apohentscheli n. sp is characterized by its large colony up to 1700 μm high, alternately branched stalk, and infundibular polykinety 3 comprising three equal-length ciliary rows. A population of Z. alternans is described in detail. Phylogenetic analyses based on SSU rDNA sequence data revealed that species with an alternately branched stalk cluster together in gene trees and probably represent an independent lineage within the genus Zoothamnium.