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  • Cockell, Charles S.; Harrison, Jesse P.; Stevens, Adam H.; Payler, Samuel J.; Hughes, Scott S.; Nawotniak, Shannon E. Kobs; Brady, Allyson L.; Elphic, R. C.; Haberle, Christopher W.; Sehlke, Alexander; Beaton, Kara H.; Abercromby, Andrew F. J.; Schwendner, Petra; Wadsworth, Jennifer; Landenmark, Hanna; Cane, Rosie; Dickinson, Andrew W.; Nicholson, Natasha; Perera, Liam; Lim, Darlene S. S. (2019)
    A major objective in the exploration of Mars is to test the hypothesis that the planet hosted life. Even in the absence of life, the mapping of habitable and uninhabitable environments is an essential task in developing a complete understanding of the geological and aqueous history of Mars and, as a consequence, understanding what factors caused Earth to take a different trajectory of biological potential. We carried out the aseptic collection of samples and comparison of the bacterial and archaeal communities associated with basaltic fumaroles and rocks of varying weathering states in Hawai'i to test four hypotheses concerning the diversity of life in these environments. Using high-throughput sequencing, we found that all these materials are inhabited by a low-diversity biota. Multivariate analyses of bacterial community data showed a clear separation between sites that have active fumaroles and other sites that comprised relict fumaroles, unaltered, and syn-emplacement basalts. Contrary to our hypothesis that high water flow environments, such as fumaroles with active mineral leaching, would be sites of high biological diversity, alpha diversity was lower in active fumaroles compared to relict or nonfumarolic sites, potentially due to high-temperature constraints on microbial diversity in fumarolic sites. A comparison of these data with communities inhabiting unaltered and weathered basaltic rocks in Idaho suggests that bacterial taxon composition of basaltic materials varies between sites, although the archaeal communities were similar in Hawai'i and Idaho. The taxa present in both sites suggest that most of them obtain organic carbon compounds from the atmosphere and from phototrophs and that some of them, including archaeal taxa, cycle fixed nitrogen. The low diversity shows that, on Earth, extreme basaltic terrains are environments on the edge of sustaining life with implications for the biological potential of similar environments on Mars and their exploration by robots and humans.
  • Zhao, Ke; Li, Jing; Shen, Meiling; Chen, Qiang; Liu, Maoke; Ao, Xiaolin; Liao, Decong; Gu, Yunfu; Xu, Kaiwei; Ma, Menggen; Yu, Xiumei; Xiang, Quanju; Chen, Ji; Zhang, Xiaoping; Penttinen, Petri (2018)
    Many actinobacteria produce secondary metabolites that include antimicrobial compounds. Since most of the actinobacteria cannot be cultivated, their antimicrobial potential awaits to be revealed. We hypothesized that the actinobacterial endophyte communities inside Melia toosendan (Chinaberry) tree are diverse, include strains with antimicrobial activity, and that antimicrobial activity can be detected using a cultivation independent approach and co-occurrence analysis. We isolated and identified actinobacteria from Chinaberry, tested their antimicrobial activities, and characterized the communities using amplicon sequencing and denaturing gradient gel electrophoresis as cultivation independent methods. Most of the isolates were identified as Streptomyces spp., whereas based on amplicon sequencing the most abundant OTU was assigned to Rhodococcus, and Tomitella was the most diverse genus. Out of the 135 isolates, 113 inhibited the growth of at least one indicator organism. Six out of the 7577 operational taxonomic units (OTUs) matched 46 cultivated isolates. Only three OTUs, Streptomyces OTU4, OTU11, and OTU26, and their corresponding isolate groups were available for comparing co-occurrences and antimicrobial activity. Streptomyces OTU4 correlated negatively with a high number of OTUs, and the isolates corresponding to Streptomyces OTU4 had high antimicrobial activity. However, for the other two OTUs and their corresponding isolate groups there was no clear relation between the numbers of negative correlations and antimicrobial activity. Thus, the applicability of co-occurrence analysis in detecting antimicrobially active actinobacteria could not be proven.
  • Ma, Yang; Qu, Zhao-Lei; Liu, Bing; Tan, Jia-Jin; Asiegbu, Fred O.; Sun, Hui (2020)
    Pine wilt disease (PWD) caused by the nematode Bursaphelenchus xylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function in the needles, roots, and soil of diseased pine were studied under field conditions using Illumina MiSeq coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved states (PICRUSt) software. The results showed that the community and functional structure of healthy and diseased trees differed only in the roots and needles, respectively (p <0.05). The needles, roots, and soil formed unique bacterial community and functional structures. The abundant phyla across all samples were Proteobacteria (41.9% of total sequence), Actinobacteria (29.0%), Acidobacteria (12.2%), Bacteroidetes (4.8%), and Planctomycetes (2.1%). The bacterial community in the healthy roots was dominated by Acidobacteria, Planctomycetes, and Rhizobiales, whereas in the diseased roots, Proteobacteria, Firmicutes, and Burkholderiales were dominant. Functionally, groups involved in the cell process and genetic information processing had a higher abundance in the diseased needles, which contributed to the difference in functional structure. The results indicate that PWD can only affect the host bacteria community structure and function in certain anatomical regions of the host tree.
  • Lopez-Echartea, Eglantina; Strejcek, Michal; Mukherjee, Shinjini; Uhlik, Ondrej; Yrjälä, Kim (2020)
    Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soils, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils had a bacterial community succession through the years, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.
  • Nordgren, Heli; Aaltonen, Kirsi; Sironen, Tarja; Kinnunen, Paula M.; Kivisto, Ilkka; Raunio-Saarnisto, Mirja; Moisander-Jylha, Anna-Maria; Korpela, Johanna; Kokkonen, Ulla-Maija; Hetzel, Udo; Sukura, Antti; Vapalahti, Olli (2014)
  • Ouwerkerk, Janneke P.; Tytgat, Hanne L. P.; Elzinga, Janneke; Koehorst, Jasper; Van den Abbeele, Pieter; Henrissat, Bernard; Gueimonde, Miguel; Cani, Patrice D.; Van de Wiele, Tom; Belzer, Clara; de Vos, Willem M. (2022)
    Akkermansia muciniphila is a champion of mucin degradation in the human gastrointestinal tract. Here, we report the isolation of six novel strains from healthy human donors and their genomic, proteomic and physiological characterization in comparison to the type-strains A. muciniphila Muc(T) and A. glycaniphila Pyt(T). Complete genome sequencing revealed that, despite their large genomic similarity (>97.6%), the novel isolates clustered into two distinct subspecies of A. muciniphila: Amuc1, which includes the type-strain Muc(T), and AmucU, a cluster of unassigned strains that have not yet been well characterized. CRISPR analysis showed all strains to be unique and confirmed that single healthy subjects can carry more than one A. muciniphila strain. Mucin degradation pathways were strongly conserved amongst all isolates, illustrating the exemplary niche adaptation of A. muciniphila to the mucin interface. This was confirmed by analysis of the predicted glycoside hydrolase profiles and supported by comparing the proteomes of A. muciniphila strain H2, belonging to the AmucU cluster, to Muc(T) and A. glycaniphila Pyt(T) (including 610 and 727 proteins, respectively). While some intrinsic resistance was observed among the A. muciniphila straind, none of these seem to pose strain-specific risks in terms of their antibiotic resistance patterns nor a significant risk for the horizontal transfer of antibiotic resistance determinants, opening the way to apply the type-strain Muc(T) or these new A. muciniphila strains as next generation beneficial microbes.
  • Andreevskaya, Margarita; Hultman, Jenni; Johansson, Per; Laine, Pia; Paulin, Lars; Auvinen, Petri; Björkroth, Johanna (2016)
    Leuconostoc gelidum subsp. gasicomitatum is a predominant lactic acid bacterium (LAB) in spoilage microbial communities of different kinds of modified-atmosphere packaged (MAP) food products. So far, only one genome sequence of a poultry-originating type strain of this bacterium (LMG 18811T) has been available. In the current study, we present the completely sequenced and functionally annotated genome of strain KG16-1 isolated from a vegetable-based product. In addition, six other vegetable-associated strains were sequenced to study possible “niche” specificity suggested by recent multilocus sequence typing. The genome of strain KG16-1 consisted of one circular chromosome and three plasmids, which together contained 2,035 CDSs. The chromosome carried at least three prophage regions and one of the plasmids encoded a galactan degradation cluster, which might provide a survival advantage in plant-related environments. The genome comparison with LMG 18811T and six other vegetable strains suggests no major differences between the meat- and vegetable-associated strains that would explain their “niche” specificity. Finally, the comparison with the genomes of other leuconostocs highlights the distribution of functionally interesting genes across the L. gelidum strains and the genus Leuconostoc.
  • Ray, Daisy; Leary, Peter; Livens, Francis; Gray, Neil; Morris, Katherine; Law, Kathleen A.; Fuller, Adam J.; Abrahamsen-Mills, Liam; Howe, John; Tierney, Kieran; Muir, Graham; Law, Gareth T.W. (2020)
    Understanding anthropogenic radionuclide biogeochemistry and mobility in natural systems is key to improving the management of radioactively contaminated environments and radioactive wastes. Here, we describe the contemporary depth distribution and phase partitioning of 137Cs, Pu, and 241Am in two sediment cores taken from the Irish Sea (Site 1: the Irish Sea Mudpatch; Site 2: the Esk Estuary). Both sites are located ~10 km from the Sellafield nuclear site. Low-level aqueous radioactive waste has been discharged from the Sellafield site into the Irish Sea for >50 y. We compare the depth distribution of the radionuclides at each site to trends in sediment and porewater redox chemistry, using trace element abundance, microbial ecology, and sequential extractions, to better understand the relative importance of sediment biogeochemistry vs. physical controls on radionuclide distribution/post-depositional mobility in the sediments. We highlight that the distribution of 137Cs, Pu, and 241Am at both sites is largely controlled by physical mixing of the sediments, physical transport processes, and sediment accumulation. Interestingly, at the Esk Estuary, microbially-mediated redox processes (considered for Pu) do not appear to offer significant controls on Pu distribution, even over decadal timescales. We also highlight that the Irish Sea Mudpatch likely still acts as a source of historical pollution to other areas in the Irish Sea, despite ever decreasing levels of waste output from the Sellafield site.
  • Eronen-Rasimus, Eeva L.; Nakki, Pinja P.; Kaartokallio, Hermanni P. (2022)
    Plastic pollution threatens both terrestrial and aquatic ecosystems. As a result of the pressures of replacing oil based materials and reducing the accumulation of litter in the environment, the use of bioplastics is increasing, despite little being known about their accurate biodegradation in natural conditions. Here, we investigated the weight attrition and degradation behavior of four different bioplastic materials compared to conventional oil-based polyethylene during a 1-year in situ incubation in the brackish Baltic Sea and in controlled 1 month biodegradation experiments in the laboratory. Bacterial communities were also investigated to verify whether putative plastic degrading bacteria are enriched on bioplastics. Poly -L-lactic acid showed no signs of degradation, whereas poly(3-hydroxybutyrate/ 3-hydroxyvalerate) (PHB/HV), plasticized starch (PR), and cellulose acetate (CA) degraded completely or almost completely during 1-year in situ incubations. In accordance, bacterial taxa potentially capable of using complex carbon substrates and belonging, e.g., to class Gammaproteobacteria were significantly enriched on PHB/HV, PR, and CA. An increase in gammaproteobacterial abundance was also observed in the biodegradation experiments. The results show substantial differences in the persistence and biodegradation rates among bioplastics, thus highlighting the need for carefully selecting materials for applications with risk of becoming marine litter.
  • Ma, Liang; Chen, Zehua; Huang, Da Wei; Cisse, Ousmane H.; Rothenburger, Jamie L.; Latinne, Alice; Bishop, Lisa; Blair, Robert; Brenchley, Jason M.; Chabe, Magali; Deng, Xilong; Hirsch, Vanessa; Keesler, Rebekah; Kutty, Geetha; Liu, Yueqin; Margolis, Daniel; Morand, Serge; Pahar, Bapi; Peng, Li; Van Rompay, Koen K. A.; Song, Xiaohong; Song, Jun; Sukura, Antti; Thapar, Sabrina; Wang, Honghui; Weissenbacher-Lang, Christiane; Xu, Jie; Lee, Chao-Hung; Jardine, Claire; Lempicki, Richard A.; Cushion, Melanie T.; Cuomo, Christina A.; Kovacs, Joseph A. (2020)
    Pneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multicopy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneurnocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins and provide a detailed description of the classification, unique characteristics, and phylogenetic relatedness of five Msg families. We further describe, for the first time, the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. coda from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests multiple functions for this superfamily rather than just conferring antigenic variation to allow immune evasion as previously believed. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology. IMPORTANCE Pneumocystis continues to be a major cause of disease in humans with immunodeficiency, especially those with HIV/AIDS and organ transplants, and is being seen with increasing frequency worldwide in patients treated with immunode-pleting monoclonal antibodies. Annual health care associated with Pneumocystis pneumonia costs similar to$475 million dollars in the United States alone. In addition to causing overt disease in immunodeficient individuals, Pneumocystis can cause subclinical infection or colonization in healthy individuals, which may play an important role in species preservation and disease transmission. Our work sheds new light on the diversity and complexity of the msg superfamily and strongly suggests that the versatility of this superfamily reflects multiple functions, including antigenic variation to allow immune evasion and optimal adaptation to host environmental conditions to promote efficient infection and transmission. These findings are essential to consider in developing new diagnostic and therapeutic strategies.
  • Chen, Yuan X.; Zou, Lan; Penttinen, Petri; Chen, Qiang; Li, Qi Q.; Wang, Chang Q.; Xu, Kai W. (2018)
    We isolated 65 rhizobial strains from faba bean (Vicia faba L.) from Panxi, China, studied their plant growth promoting ability with nitrogen free hydroponics, genetic diversity with clustered analysis of combined ARDRA and IGS-RFLP, and phylogeny by sequence analyses of 16S rRNA gene, three housekeeping genes and symbiosis related genes. Eleven strains improved the plant shoot dry mass significantly comparing to that of not inoculated plants. According to the clustered analysis of combined ARDRA and IGS-RFLP the isolates were genetically diverse. Forty-one of 65 isolates represented Rhizobium anhuiense, and the others belonged to R. fabae, Rhizobium vallis, Rhizobium sophorae, Agrobacterium radiobacter, and four species related to Rhizobium and Agrobacterium. The isolates carried four and five genotypes of nifH and nodC, respectively, in six different nifH-nodC combinations. When looking at the species-nifH-nodC combinations it is noteworthy that all but two of the six R. anhuiense isolates were different. Our results suggested that faba bean rhizobia in Panxi are diverse at species, plant growth promoting ability and symbiosis related gene levels.
  • Andreevskaya, Margarita; Jääskelainen, Elina; Johansson, Per; Ylinen, Anne; Paulin, Lars; Björkroth, Johanna; Auvinen, Petri (2018)
    Psychrotrophic lactic acid bacteria (LAB) are the prevailing spoilage organisms in packaged cold-stored meat products. Species composition and metabolic activities of such LAB spoilage communities are determined by the nature of the meat product, storage conditions, and interspecies interactions. Our knowledge of system level responses of LAB during such interactions is very limited. To expand it, we studied interactions between three common psychrotrophic spoilage LAB (Leuconostoc gelidum, Lactococcus piscium, and Lactobacillus oligofermentans) by comparing their time course transcriptome profiles obtained during their growth in individual, pairwise, and triple cultures. The study revealed how these LAB employed different strategies to cope with the consequences of interspecies competition. The fastest-growing bacterium, Le. gelidum, attempted to enhance its nutrient-scavenging and growth capabilities in the presence of other LAB through upregulation of carbohydrate catabolic pathways, pyruvate fermentation enzymes, and ribosomal proteins, whereas the slower-growing Lc. piscium and Lb. oligofermentans downregulated these functions. These findings may explain the competitive success and predominance of Le. gelidum in a variety of spoiled foods. Peculiarly, interspecies interactions induced overexpression of prophage genes and restriction modification systems (mechanisms of DNA exchange and protection against it) in Lc. piscium and Lb. oligofermentans but not in Le. gelidum. Cocultivation induced also overexpression of the numerous putative adhesins in Lb. oligofermentans. These adhesins might contribute to the survival of this slowly growing bacterium in actively growing meat spoilage communities. IMPORTANCE Despite the apparent relevance of LAB for biotechnology and human health, interactions between members of LAB communities are not well known. Knowledge of such interactions is crucial for understanding how these communities function and, consequently, whether there is any possibility to develop new strategies to interfere with their growth and to postpone spoilage of packaged and refrigerated foods. With the help of controlled experiments, detailed regulation events can be observed. This study gives an insight into the system level interactions and the different competition-induced survival strategies related to enhanced uptake and catabolism of carbon sources, overexpression of adhesins and putative bacteriocins, and the induction of exchange of genetic material. Even though this experiment dealt with only three LAB strains in vitro, these findings agreed well with the relative abundance patterns typically reported for these species in natural food microbial communities.
  • Launis, Annina; Pykälä, Juha; van den Boom, Pieter; Serusiaux, Emmanuel; Myllys, Leena (2019)
    In this study we clarify the phylogeny and reassess the current taxonomy of the Micarea prasina group, focusing especially on the M. byssacea and M. micrococca complexes. The phylogeny was investigated using ITS, mtSSU and Mcm7 regions from 25 taxa belonging to the M. prasina group. A total of 107 new sequences were generated. Data were analyzed using maximum parsimony and maximum likelihood methods. The results reveal five undescribed well-supported lineages. Four of the lineages represent new species described as Micarea pseudomicrococca Launis & Myllys sp. nov., M. czarnotae Launis, van den Boom, Serusiaux & Myllys sp. nov., M. microareolata Launis, Pykala & Myllys sp. nov. and M. laeta Launis & Myllys sp. nov. In addition, a fifth lineage was revealed that requires further study. Micarea pseudomicrococca is characterized by an olive green granular thallus, small cream-white or brownish apothecia lacking the Sedifolia-grey pigment and two types of paraphyses up to 2 mu m wide. Micarea czarnotae forms a granular, densely granular or continuous olive green thallus, convex to hemispherical apothecia often with the Sedifolia-grey pigment and no crystalline granules in the thallus. Micarea microareolata is characterized by a +/- pale green areolate thallus (composed of goniocysts), cream-white apothecia lacking the Sedifolia-grey pigment and narrow spores. Micarea laeta has a vivid to olive green granular thallus, pale apothecia lacking the Sedifolia-grey pigment and wider spores compared to M. microareolata. Descriptions, images and a key are provided for the new species. Crystalline granules are introduced as a novel species-level character for Micarea.
  • Zou, Lan; Chen, Yuan Xue; Penttinen, Petri; Lan, Qin; Wang, Ke; Liu, Ming; Peng, Dan; Zhang, Xiaoping; Chen, Qiang; Zhao, Ke; Zeng, Xiangzhong; Xu, Kai Wei (2016)
    Thirty-one nodulating rhizobium strains were collected from root nodules of spring and winter type faba bean cultivars grown in micro ecoarea, i.e. the same field in Chengdu plain, China. The symbiotic efficiency and phylogeny of these strains were studied. Effectively nitrogen fixing strains were isolated from both winter type and spring type cultivars. Based on phylogenetic analysis of 16S rRNA gene and concatenated sequence of atpD, glnII and recA genes, the isolates were assigned as Rhizobium anhuiense and a potential new Rhizobium species. The isolates were diverse on symbiosis related gene level, carrying five, four and three variants of nifH, nodC and nodD, respectively. Strains carrying similar gene combinations were trapped by both winter and spring cultivars, disagreeing with the specificity of symbiotic genotypes to reported earlier faba bean ecotypes.
  • Asfaw, Beimnet; Aserse, Aregu Amsalu; Asefa, Fassil; Yli-Halla, Markku; Lindstrom, Kristina (2020)
    In total 196 bacterial isolates were obtained from root nodules of lentil (Lens culinaris) and faba bean (Vicia faba) grown on soil samples collected from 10 different sites in central and southern parts of Ethiopia. All isolates were identified as members of the genus Rhizobium by using recA gene sequence analysis. In the recA phylogenetic tree 195 rhizobial strains were classified into nine genospecies. The phylogeny of symbiotic genes nodC and nifH revealed five and six distinct groups respectively, largely dominated by symbiovar viciae. A multivariate analysis showed that environmental variables of the sampling sites considered in this study had more effect on the distribution and composition of the genospecies than the host legumes of the strains. Twenty representative strains, selected based on their isolation site, host plant and nodC group, were able to nodulate all lentil, faba bean, field pea (Pisum abyssinicum) and grass pea (Lathyrus sativus) plants in a greenhouse test in axenic conditions. The majority of the rhizobial strains were effective nitrogen-fixing symbionts for all tested legumes, indicating their potential to serve as broad host-range inoculants in agriculture. The present work suggests the presence of taxonomically and symbiotically diverse rhizobial species for legumes in the Viciae tribe in Ethiopia.
  • Geerlings, Sharon Y.; Ouwerkerk, Janneke P.; Koehorst, Jasper J.; Ritari, Jarmo; Aalvink, Steven; Stecher, Bärbel; Schaap, Peter J.; Paulin, Lars; de Vos, Willem M.; Belzer, Clara (2021)
    Background Akkermansia muciniphila is a member of the human gut microbiota where it resides in the mucus layer and uses mucin as the sole carbon, nitrogen and energy source. A. muciniphila is the only representative of the Verrucomicrobia phylum in the human gut. However, A. muciniphila 16S rRNA gene sequences have also been found in the intestines of many vertebrates. Results We detected A. muciniphila-like bacteria in the intestines of animals belonging to 15 out of 16 mammalian orders. In addition, other species belonging to the Verrucomicrobia phylum were detected in fecal samples. We isolated 10 new A. muciniphila strains from the feces of chimpanzee, siamang, mouse, pig, reindeer, horse and elephant. The physiology and genome of these strains were highly similar in comparison to the type strain A. muciniphila Muc(T). Overall, the genomes of the new strains showed high average nucleotide identity (93.9 to 99.7%). In these genomes, we detected considerable conservation of at least 75 of the 78 mucin degradation genes that were previously detected in the genome of the type strain Muc(T). Conclusions The low genomic divergence observed in the new strains may indicate that A. muciniphila favors mucosal colonization independent of the differences in hosts. In addition, the conserved mucus degradation capability points towards a similar beneficial role of the new strains in regulating host metabolic health.
  • Sinkko, Hanna; Hepolehto, Iina; Lyra, Christina; Rinta-Kanto, Johanna M.; Villnäs, Anna; Norkko, Joanna; Norkko, Alf; Timonen, Sari (2019)
    Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.
  • Roslund, Marja; Puhakka, Riikka; Nurminen, Noora; Oikarinen, Sami; Siter, Nathan; Grönroos, Mira; Cinek, Ondrej; Kramna, Lenka; Jumpponen, Ari; Laitinen, Olli; Rajaniemi, Juho; Hyöty, Heikki; Sinkkonen, Aki (2021)
    Background: In modern urban environments children have a high incidence of inflammatory disorders, including allergies, asthma, and type 1 diabetes. The underlying cause of these disorders, according to the biodiversity hypothesis, is an imbalance in immune regulation caused by a weak interaction with environmental microbes. In this 2-year study, we analyzed bacterial community shifts in the soil surface in day-care centers and commensal bacteria inhabiting the mouth, skin, and gut of children. We compared two different day-care environments: standard urban day-care centers and intervention day-care centers. Yards in the latter were amended with biodiverse forest floor vegetation and sod at the beginning of the study. Results: Intervention caused a long-standing increase in the relative abundance of nonpathogenic environmental mycobacteria in the surface soils. Treatment-specific shifts became evident in the community composition of Gammaproteobacteria, Negativicutes, and Bacilli, which jointly accounted for almost 40 and 50% of the taxa on the intervention day-care children's skin and in saliva, respectively. In the year-one skin swabs, richness of Alpha-, Beta-, and Gammaproteobacteria was higher, and the relative abundance of potentially pathogenic bacteria, including Haemophilus parainfluenzae, Streptococcus sp., and Veillonella sp., was lower among children in intervention day-care centers compared with children in standard day-care centers. In the gut, the relative abundance of Clostridium sensu stricto decreased, particularly among the intervention children. Conclusions: This study shows that a 2-year biodiversity intervention shapes human commensal microbiota, including taxa that have been associated with immune regulation. Results indicate that intervention enriched commensal microbiota and suppressed the potentially pathogenic bacteria on the skin. We recommend future studies that expand intervention strategies to immune response and eventually the incidence of immune-mediated diseases.
  • Hiippala, Kaisa; Kainulainen, Veera; Kalliomaki, Marko; Arkkila, Perttu; Satokari, Reetta (2016)
    Sutterella species have been frequently associated with human diseases, such as autism, Down syndrome, and inflammatory bowel disease (IBD), but the impact of these bacteria on health still remains unclear. Especially the interactions of Sutterella spp. with the host are largely unknown, despite of the species being highly prevalent. In this study, we addressed the interaction of three known species of Sutterella with the intestinal epithelium and examined their adhesion properties, the effect on intestinal barrier function and the pro-inflammatory capacity in vitro. We also studied the relative abundance and prevalence of the genus Sutterella and Sutterella wadsworthensis in intestinal biopsies of healthy individuals and patients with celiac disease (CeD) or IBD. Our results show that Sutterella spp. are abundant in the duodenum of healthy adults with a decreasing gradient toward the colon. No difference was detected in the prevalence of Sutterella between the pediatric IBD or CeD patients and the healthy controls. Sutterella parvirubra adhered better than the two other Sutterella spp. to differentiated Caco-2 cells and was capable of decreasing the adherence of S. wadsworthensis, which preferably bound to mucus and human extracellular matrix proteins. Furthermore, only S. wadsworthensis induced an interleukin-8 production in enterocytes, which could be due to different lipopolysaccharide structures between the species. However, its pro-inflammatory activity was modest as compared to non-pathogenic Escherichia coli. Sutterella spp. had no effect on the enterocyte monolayer integrity in vitro. Our findings indicate that the members of genus Sutterella are widely prevalent commensals with mild pro-inflammatory capacity in the human gastrointestinal tract and do not contribute significantly to the disrupted epithelial homeostasis associated with microbiota dysbiosis and increase of Proteobacteria. The ability of Sutterella spp. to adhere to intestinal epithelial cells indicate that they may have an immunomodulatory role.
  • Thi Phuong Nam Bui; Schols, Henk A.; Jonathan, Melliana; Stams, Alfons J. M.; de Vos, Willem M.; Plugge, Caroline M. (2019)
    The human intestinal tract harbors diverse and complex microbial communities that have a vast metabolic capacity including the breakdown of complex carbohydrates into short chain fatty acids, acetate, propionate, and butyrate. As butyrate is beneficial for gut health there is much attention on butyrogenic bacteria and their role in the colonic anaerobic food chain. However, our understanding how production of butyrate by gut microorganisms is controlled by interactions between different species and environmental nutrient availability is very limited. To address this, we set up experimental in vitro co-culture systems to study the metabolic interactions of Anaerostipes rhamnosivorans, a butyrate producer with each of its partners; Blautia hydrogenotrophica, an acetogen; Methanobrevibacter smithii, a methanogen and Bacteroides thetaiotaomicron, a versatile degrader of plant cell wall pectins; through corresponding specific cross-feeding. In all co-cultures, A. rhamnosivorans was able to benefit from its partner for enhanced butyrate formation compared to monocultures. Interspecies transfer of hydrogen or formate from A. rhamnosivorans to the acetogen B. hydrogenotrophica and in turn of acetate from the acetogen to the butyrogen were essential for butyrate formation. A. rhamnosivorans grown on glucose supported growth of M. smithii via interspecies formate/hydrogen transfer enhancing butyrate formation. In the co-culture with pectin, lactate was released by B. thetaiotaomicron which was concomitantly used by A. rhamnosivorans for the production of butyrate. Our findings indicate enhanced butyrate formation through microbe-microbe interactions between A. rhamnosivorans and an acetogen, a methanogen or a pectin-degrader. Such microbial interactions enhancing butyrate formation may be beneficial for colonic health.