Reuse of composted food waste from rural China as vermicomposting substrate: effects on earthworms, associated microorganisms, and economic benefits

ABSTRACTAerobic composting of food waste (FW) from rural China using a composting device results in a substantial financial burden on the government. This study aimed to assess the feasibility of mitigating this cost using vermicomposting of composted FW. The specific aims were to elucidate the effects of composted FW on earthworm growth and reproduction, reveal the changes in the physical and chemical properties of earthworm casts during vermicomposting, identify the microbial community structure associated with vermicomposting, and perform a financial analysis based on the yield of earthworms and earthworm casts. Mixing composted FW and mature cow dung in an equal ratio achieved the highest earthworm reproduction rate, where 100 adult earthworms produced 567 juvenile earthworms and 252 cocoons in 40 d. Earthworms reduce salt content of vermicomposting substrates by assimilating Na+ and promoting humification by transforming humin into humic and fulvic acid, thus producing earthworm casts with a high generation index > 80%. When composted FW was added to a vermicomposting substrate, a distinctive microbial community structure with alkaliphilic, halophilic, and lignocellulolytic microorganisms dominated the microflora. The dominant bacterial species was Saccharopolyspora rectivirgula, and the dominant fungal species changed from Kernia nitida to Coprinopsis scobicola. Furthermore, microbial genes for refractory organic matter and fat degradation were observed in Vibrio cholerae, Kernia nitida, and Coprinopsis scobicola. Financial analysis showed that vermicomposting has the potential to reduce the cost associated with FW disposal from $ 57 to $ 18/t.

Plastisphere characterization in habitat of the highly endangered Shinisaurus crocodilurus: Bacterial composition, assembly, function and the comparison with surrounding environment

Plastisphere is a new niche for microorganisms that complicate the ecological effects of plastics, and may profoundly influence biodiversity and habitat conservation. The DaGuishan National Nature Reserve, one of the largest habitats of the highly endangered crocodile lizard (Shinisaurus crocodilurus), is experiencing plastic pollution without sufficient attention. Here, plastisphere collected from captive tanks of crocodile lizards in this nature reserve was characterized for the first time. Three types of plastic (PE-PP, PE1, and PE2) together with the surrounding water and soil samples, were collected, and 16S rRNA sequencing technology was used to characterize the bacterial composition. The results demonstrated that plastisphere was driven by stochastic process and had a distinct bacterial community with higher diversity than that in surrounding water (p < 0.05). Bacteria related to nitrogen and carbon cycles (Pseudomonas psychrotolerans, Methylobacterium-Methylorubrum) were more abundant in plastisphere than in water or soil (p < 0.05). More importantly, plastics recruited pathogens and those bacteria function in antibiotic resistant genes (ARGs) coding. Bacteria related to polymer degradation also proliferated in plastisphere, especially Bacillus subtilis with a fold change of 42.01. The PE2 plastisphere, which had the lowest diversity and was dominated by Methylobacterium-Methylorubrum differed from PE 1 and PE-PP plastispheres totally. Plastics' morphology and aquatic nutrient levels contributed to the heterogeneity of different plastispheres. Overall, this study demonstrated that plastispheres diversify in composition and function, affecting ecosystem services directly or indirectly. Pathogens and bacteria related to ARGs expression enriched in the plastisphere should not be ignored because they may threaten the health of crocodile lizards by increasing the risk of infection. Plastic pollution control should be included in conservation efforts for crocodile lizards. This study provides new insights into the potential impacts of plastisphere, which is important for ecological risk assessments of plastic pollution in the habitats of endangered species.

Human actinomycetoma caused by Actinomadura mexicana in Sudan: the first report

Mycetoma is a localized, chronic, granulomatous disease that can be caused by fungi (eumycetoma) or bacteria (actinomycetoma). Of the 70 different causative agents implicated in mycetoma worldwide, Actinomadura madurae is the only one that causes multiple cases on all continents. Recently, new Actinomadura species were described as causative agents of human mycetoma. One of these new causative agents was Actinomadura mexicana, which was identified in Latin America. Here we demonstrate that this causative agent is not confined to Latin America and that it is also a causative agent of actinomycetoma in Sudan. The disease was managed by antibiotic treatment alone and resulted in complete cure after 6 months of treatment, which is quick when compared with actinomycetoma cases caused by other Actinomadura species.

Actinomadura roseirufa sp. nov., producer of semduramicin, a polyether ionophore

The taxonomic position of 'Actinomadura roseorufa' LMG 30035^T, a semduramicin-producing mutant of strain ATCC 53666^P, which was isolated from a soil sample collected in Yamae Village, Kamamoto, Japan, was clarified in the present study using a polyphasic approach. This Gram-positive, aerobic actinomycete formed a well-developed, extensively branched, non-fragmenting substrate and aerial mycelia which differentiated into single, smooth-appearing spores. Based on analysis of nearly complete 16S rRNA gene sequence, strain LMG 30035^T was found to be closely related to the type strains of Actinomadura fibrosa ATCC 49459^T (98.88 %) and Actinomadura formosensis JCM 7474^T (98.82 %) (pairwise similarity values in parentheses). Digital DNA-DNA hybridisation experiments revealed unambiguously that strain LMG 30035^T represents a novel Actinomadura species (OrthoANIu values less than 83.1 %; dDDH values less than 27.2 % with type strains of validly named Actinomadura species). Analysis of the cell wall revealed the presence of meso-diaminopimelic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, galactose, ribose and rhamnose. The major polar lipids included phosphatidylinositol and diphosphatidylglycerol. The predominant menaquinones were MK-9(H₆), MK-9(H₈), MK-9(H₄) and MK-9(H₂). The major fatty acids were C_16 : 00, 10-methyl C_18 : 0, C_18 : 1  ω9c and C_18 : 00. The DNA G+C content of its genome was 72.5 mol%. In summary, these characteristics distinguish strain LMG 30035^T from validly named species of the genus Actinomadura, and therefore, we propose to classify this strain formally as the novel species Actinomadura roseirufa sp. nov. with LMG 30035^T (=CECT 9808^T,=ATCC 53664^T) as the type strain.

Actinomadura barringtoniae sp. nov., an endophytic actinomycete isolated from the roots of Barringtonia acutangula (L.) Gaertn

A novel actinomycete strain, designated GKU 128^T, isolated from the roots of an Indian oak tree [Barringtonia acutangula (L.) Gaertn.] at Khao Khitchakut district, Chantaburi province, Thailand, was characterized by using a polyphasic approach. The strain formed a branched substrate and aerial mycelia which differentiated into straight to flexuous chains of smooth-ornamented spores. Analysis of the cell wall revealed the presence of meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, mannose, rhamnose and ribose. Mycolic acids were absent. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside. The predominant menaquinones were MK-9(H6), MK-9(H8), MK-9(H0) and MK-9(H4). The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). The genomic DNA G+C content was 70.5 mol%. Based on 16S rRNA gene sequence analysis, strain GKU 128^T was closely related to the type strains of Actinomadura nitritigenes NBRC 15918^T (99.2 % sequence similarity) and Actinomadura fibrosa JCM 9371^T (98.7 %). The levels of DNA-DNA relatedness between strain GKU 128^T and the closely related type species were less than 19 %. On the basis of phenotypic and genotypic characteristics, strain GKU 128^T could be distinguished from its closely related type strains and represents a novel species of the genus Actinomadura, for which the name Actinomadura barringtoniae sp. nov. (=TBRC 7225^T=NBRC 113074^T) is proposed.

Aerobic Actinomycetes of Clinical Significance

The group of Gram-positive bacillary organisms broadly known as "aerobic actinomycetes" consists of heterogeneous and taxonomically divergent genera. They are found in a wide variety of natural and man-made environments but are rarely considered a part of the normal human flora, with infections normally originating from exogenous sources. An extensive number of genera have been described, but only a minority of these has been associated with human or veterinary health. The association with human disease is usually of an opportunistic nature, either through accidental means of inoculation or through involvement with immunocompromising conditions in the host. They cause a wide spectrum of diseases in humans, which may differ greatly between the genera and even between species, but which also may have a great amount of overlap. The occurrence of such infections is probably greater than appreciated, since many may go unrecognized. Etiologic prevalence of specific genera and species varies geographically within the United States and worldwide. Traditional phenotypic identification methods for separation of the many genera and species of aerobic actinomycetes have found great difficulties. Recent use of chemotaxonomic analyses and emerging technologies such as molecular analysis of nucleic acids, and more recently proteomics for identification to the genus/species level, has provided a far more robust technique to understand the organisms' relatedness, distribution, epidemiology, and pathogenicity in humans.

Actinomadura alkaliterrae sp. nov., isolated from an alkaline soil

A polyphasic study was undertaken to establish the taxonomic status of an Actinomadura strain isolated from the margin of a saline, alkaline lake in Central Anatolia, Turkey. Strain D310AT^T was shown to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Actinomadura such as hooked or irregular spiral spore chains, meso-diaminopimelic acid as the major cell wall diaminopimelic acid, and diphosphatidylglycerol and phosphatidylinositol as major polar lipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain D310AT^T is closely, albeit loosely, associated with Actinomadura darangshiensis DLS-70^T with 97.2% sequence similarity, but was readily separated from the latter using diverse phenotypic properties. Consequently, the isolate is considered to represent a new species of Actinomadura for which the name Actinomadura alkaliterrae sp. nov. is proposed, with the type strain D310AT^T (=DSM 101185^T = KCTC 39657^T).

Actinomadura Species: Laboratory Maintenance and Ribosome Engineering

Actinomadura spp. are aerobic, Gram-positive, catalase-positive, non-acid fast, non-motile actinomycetes. Some species of Actinomadura are associated with opportunistic infections in humans. However, many bioactive compounds with pharmaceutical applications can be isolated from various Actinomadura spp. This unit includes general protocols for the laboratory maintenance of Actinomadura spp., including growth in liquid medium, growth on solid agar, long-term storage, and generation of a higher producing strain by ribosome engineering. Actinomadura hibisca P157-2 is used as a prototype for explaining the considerations for efficient laboratory maintenance of Actinomadura spp. © 2017 by John Wiley & Sons, Inc.

Actinomadura adrarensis sp. nov., an actinobacterium isolated from Saharan soil

A novel actinobacterial strain, designated ACD12^T, was isolated from a Saharan soil sample collected from Adrar province, southern Algeria. A polyphasic study was carried out to establish the taxonomic position of this strain. Strain ACD12^T was observed to form extensively branched substrate mycelia. Aerial mycelium was absent or was weakly produced on all media tested, while spore chains were short with a hooked and irregular spiral form (2-3 turns). The dominant diaminopimelic acid isomer in the cell wall was meso-diaminopimelic acid. Glucose, ribose, galactose, mannose and madurose occured in whole-cell hydrolysates. The major phospholipid was diphosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was MK-9(H6). The fatty acid profile was characterized by the presence of C16 : 0, C17 : 0, C15 : 0, C18 : 0, C18 : 1 cis9 and iso-C16 : 0. Results of 16S rRNA gene sequence comparisons revealed that strain ACD12^T shared the highest degree of 16S rRNA gene sequence similarity with Actinomadura sputi DSM 45233^T (98.3 %) and Actinomadura hallensis DSM 45043^T (97.8 %). All tree-making algorithms used also supported strain ACD12^T forming a distinct clade with its most closely related species. In addition, DNA-DNA hybridization indicated only 39.8 % relatedness with A. sputi DSM 45233^T and 18.7 % relatedness with A. hallensis DSM 45043^T. The combined phenotypic and genotypic data show that the novel isolate represents a novel species of the genus Actinomadura, for which the name Actinomadura adrarensis sp. nov., is proposed, with the type strain ACD12^T (=DSM 46745^T =CECT 8842^T).

Actinomadura algeriensis sp. nov., an actinobacterium isolated from Saharan soil

During the course of a screening programme for new taxa of actinobacteria, a strain designated ACD1(T), was isolated from a Saharan soil in the Hoggar region (Algeria). The taxonomic position of this strain was determined using a polyphasic taxonomic approach. The strain was observed to form extensively branched, non-fragmenting substrate mycelium, and aerial mycelium with straight to flexuous, hooked and irregular spirals (1-2 turns) forming short chains of spores. The diamino acid present in the cell wall is meso-diaminopimelic acid. Galactose, glucose, madurose, mannose and ribose occur in whole-cell hydrolysates. The diagnostic phospholipids detected were diphosphatidylglycerol and phosphatidylinositol. The major menaquinones were identified as MK-9 (H4) and MK-9 (H2). The major fatty acids were found to be C16:0, C18:1 cis9, iso-C16:0 and 10-methyl C18:0. Phylogenetic analysis based on the 16S rRNA gene showed that the strain belongs to the genus Actinomadura, and is closely related to Actinomadura sediminis DSM 45500(T) (98.5 % similarity) and Actinomadura cremea subsp. cremea DSM 43676(T) (98.3 % similarity). However, DNA-DNA hybridization revealed only 48.0 % relatedness with A. sediminis DSM 45500(T) and 33.2 % relatedness with A. cremea subsp. cremea DSM 43676(T). The combined phenotypic and genotypic data showed that the strain represents a novel species of the genus Actinomadura, for which the name Actinomadura algeriensis sp. nov. is proposed, with the type strain ACD1(T) (= DSM 46744(T) = CECT 8841(T)).

Actinomadura syzygii sp. nov., an endophytic actinomycete isolated from the roots of a jambolan plum tree (Syzygium cumini L. Skeels)

The taxonomic position of an endophytic actinomycete, strain GKU 157T, isolated from the roots of a jambolan plum tree (Syzygium cumini L. Skeels) collected at Khao Khitchakut National Park, Chantaburi province, Thailand, was determined using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed that strain GKU 157T belongs to the genus Actinomadura and formed a distinct phyletic line with Actinomadura chibensis NBRC 106107T (98.6 % similarity). Strain GKU 157T formed an extensively branched, non-fragmenting substrate mycelium and aerial hyphae that differentiated into hooked to short spiral chains of about 20 non-motile spores with a warty surface. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were galactose, glucose, madurose, mannose and ribose. The N-acyl type of muramic acid was acetyl. Mycolic acids were absent. The phospholipids included phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylinositol (PI), phosphatidylinositolmannoside (PIM) and two unknown phospholipids (PLs). The major menaquinone was MK-9(H6) and the predominant fatty acids were C16:0, iso-C16:0, C18:1ω9c, C18:0 and 10-methyl C18:0 (tuberculostearic acid). The genomic DNA G+C content was 73.1 mol%. A combination of DNA–DNA hybridization results and significant differences from related species in cultural, physiological and chemical characteristics indicated that strain GKU 157T represents a novel species of the genus Actinomadura, for which the name Actinomadura syzygii sp. nov. is proposed. The type strain is GKU 157T ( = BCC 70456T = NBRC 110399T).

Actinomadura geliboluensis sp. nov., isolated from soil

A novel actinobacterium, strain A8036T, isolated from soil, was investigated by using a polyphasic taxonomic approach. The organism formed extensively branched substrate hyphae that generated spiral chains of spores with irregular surfaces. The cell wall contained meso-diaminopimelic acid (type III) and cell-wall sugars were glucose, madurose, mannose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H4). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C16 : 0, C17 : 1 cis9, C16 : 0, C15 : 0 and 10-methyl C17 : 0. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain A8036T were Actinomadura meyerae DSM 44715T (99.23 % similarity), Actinomadura bangladeshensis DSM 45347T (98.9 %) and Actinomadura chokoriensis DSM 45346T (98.3 %). However, DNA–DNA relatedness and phenotypic data demonstrated that strain A8036T could be clearly distinguished from the type strains of all closely related Actinomadura species. Strain A8036T is therefore considered to represent a novel species of the genus Actinomadura , for which the name Actinomadura geliboluensis sp. nov. is proposed. The type strain is A8036T ( = DSM 45508T = KCTC 19868T).

Actinomadura rupiterrae sp. nov., isolated from cliff soil

A novel actinomycete strain, designated CS5-AC15T, was isolated from a soil sample collected from a cliff on Mara Island, Jeju, Republic of Korea, and subjected to a polyphasic taxonomic analysis. The isolate produced well-developed, yellow substrate mycelium and white aerial mycelium that differentiated into straight or flexuous chains of smooth-surfaced spores. 16S rRNA gene sequence analyses showed that the organism belonged to the family Thermomonosporaceae and formed a tight cluster with the type strain of Actinomadura oligospora (97.4 % sequence similarity). Chemotaxonomic characteristics were consistent with its assignment to the genus Actinomadura in that the isolate had meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall, madurose as the characteristic sugar, N-acetyl type of murein in the peptidoglycan, MK-9(H6) and MK-9(H8) as major menaquinones and a polar lipid profile containing diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown phospholipids. Mycolic acids were not detected. The predominant fatty acids were C16 : 0, C18 : 1ω9c and iso-C16 : 0. The DNA G+C content was 70.9 mol%. DNA relatedness of strain CS5-AC15T and A. oligospora JCM 10648T was 37.9±0.7 %. On the basis of the phenotypic, phylogenetic and DNA–DNA hybridization data, strain CS5-AC15T is assigned to a novel species of the genus Actinomadura, for which the name Actinomadura rupiterrae sp. nov. is proposed (type strain CS5-AC15T  = KCTC 19559T  = DSM 45251T).

Actinomadura meyerae osteitis following wound contamination with hay in a woman in France: a case report

Introduction

Mycetoma is a chronic granulomatous infection caused by environmental fungi or bacteria. It affects dermal and subcutaneous tissues, with putative contiguous extension to muscles or bones. While common in tropical and subtropical areas, mycetoma is rare in Europe.

Case presentation

We describe a case of Actinomadura meyerae osteitis in a 49-year-old Caucasian woman who suffered a tibia open fracture contaminated with hay; to the best of our knowledge the first case of autochthonous A. meyerae infection reported in France. The bacterium was cultivated from a bone biopsy. Following surgical osteosynthesis and six months of treatment with cotrimoxazole, our patient made a full recovery.

Conclusion

Our case report suggests that A. meyerae is a potential agent of wound infection in farm workers in contact with hay.

Actinomadura apis sp. nov., isolated from a honey bee (Apis mellifera) hive, and the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as Actinomadura rifamycini (Gauze et al. 1987) sp. nov., comb. nov

A Gram-reaction-positive aerobic actinomycete, designated strain IM17-1(T), was isolated from a honey bee (Apis mellifera) hive in Chiang Mai Province, Thailand. The strain formed a branched substrate mycelium and mature aerial mycelium bore short chains of arthrospores with warty surfaces. The cell wall contained meso-2,6-diaminopimelic acid (cell-wall type III) and the whole cell sugars were fucose, galactose, glucose, madurose, mannose and ribose. The major isoprenoid quinone was hexahydrogenated menaquinone with nine isoprene units and the predominant cellular fatty acids were C₁₆:₀ (33.8 %), C₁₈:₁ω9c (32.7 %), summed feature 3 (C₁₆:₁ω7c and/or iso-C₁₅:₀ 2-OH) (8.7 %) and 10-methyl C₁₈:₀ (8.2 %). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. These morphological and chemotaxonomic characteristics were consistent with the classification of IM17-1(T) within the genus Actinomadura. Based on 16S rRNA gene sequence analysis, strain IM17-1(T) was closely related to the type strains of Actinomadura cremea subsp. cremea (98.1 %) and Actinomadura cremea subsp. rifamycini (98.6 %); however, it represented a distinct phylogenetic lineage from the other species within this genus. The unique genetic characteristics were reaffirmed by low levels of DNA-DNA relatedness between strain IM17-1(T) and the two most closely related type strains, A. cremea subsp. cremea JCM 3308(T) (56.5±4.9 %) and A. cremea subsp. rifamycini JCM 3309(T) (31.0±22.6 %), and further supported the proposal of IM17-1(T) as a novel species. Strain IM17-1(T) ( = JCM 16576(T)  = TISTR 1980(T)) thus represents a novel species of the genus Actinomadura, for which the name Actinomadura apis sp. nov. is proposed. In addition, the genotypic and phenotypic data suggested the reclassification of Actinomadura cremea subsp. rifamycini Gauze et al. 1987 as a separate species, Actinomadura rifamycini sp. nov., comb. nov.