Prophages as a part of Staphylococcus aureus genome contribute to the genetic diversity as well as survival strategies of their host. Some S. aureus prophages also have an imminent risk of host cell lysis and become a lytic phage. Nonetheless, interactions among S. aureus prophages, lytic phages, and their hosts, as well as the genetic diversity of S. aureus prophages, remain unclear. We identified 579 intact and 1,389 incomplete prophages in the genomes of 493 S. aureus isolates obtained from the NCBI database. The structural diversity and gene content of intact and incomplete prophages were investigated and compared with 188 lytic phages. Mosaic structure comparison, ortholog group clustering, phylogenetic analysis, and recombination network analysis were performed to estimate genetic relatedness among S. aureus intact prophages, incomplete prophages, and lytic phages. The intact and incomplete prophages harbored 148 and 522 distinct mosaic structures, respectively. The major difference between lytic phages and prophages was the lack of functional modules and genes. Compared to the lytic phages, both the S. aureus intact and incomplete prophages harbored multiple antimicrobial resistance (AMR) and virulence factor (VF) genes. Several functional modules of lytic phages 3_AJ_2017 and 23MRA shared more than 99% nucleotide sequence identity with S. aureus intact (ST20130943_p1 and UTSW_ MRSA_55_ip3) and incomplete prophages (SA3_LAU_ip3 and MRSA_FKTN_ip4); other modules showed little nucleotide sequence similarity. Ortholog and phylogenetic analyses revealed a common gene pool shared between the prophages and lytic Siphoviridae phages. Moreover, most shared sequences existed within intact (43428/137294, 31.6%) and incomplete prophages (41248/137294, 30.0%). Therefore, the maintenance or loss of functional modules in intact and incomplete prophages is key to balance the costs and benefits of large prophages harboring various AMR and VF genes in the bacterial host. The shared identical functional modules between S. aureus lytic phages and prophages are likely to result in the exchange, acquisition, and loss of functional modules, and therefore contribute to their genetic diversity. Moreover, constant recombination events within prophages globally were responsible for the coevolution of lytic phages and their bacterial hosts.
The study of bacteriophages is experiencing a resurgence owing to their antibacterial efficacy, lack of side effects, and low production cost. Nonetheless, the interactions between Staphylococcus aureus bacteriophages and their hosts remain unexplored. In this study, whole-genome sequences of 188 S. aureus bacteriophages-20 Podoviridae, 56 Herelleviridae, and 112 Siphoviridae-were obtained from the National Center for Biotechnology Information (NCBI, USA) genome database. A phylogenetic tree was constructed to estimate their genetic relatedness using single-nucleotide polymorphism analysis. Comparative analysis was performed to investigate the structural diversity and ortholog groups in the subdividing clusters. Mosaic structures and gene content were compared in relation to phylogeny. Phylogenetic analysis revealed that the bacteriophages could be distinguished into three lineages (I-III), including nine subdividing clusters and seven singletons. The subdividing clusters shared similar mosaic structures and core ortholog clusters, including the genes involved in bacteriophage morphogenesis and DNA packaging. Notably, several functional modules of bacteriophages 187 and 2368A shared more than 95% nucleotide sequence identity with prophages in the S. aureus strain RJ1267 and the Staphylococcus pseudintermedius strain SP_11306_4, whereas other modules exhibited little nucleotide sequence similarity. Moreover, the cluster phages shared similar types of holins, lysins, and DNA packaging genes and harbored diverse genes associated with DNA replication and virulence. The data suggested that the genetic diversity of S. aureus bacteriophages was likely due to gene replacement, acquisition, and loss among staphylococcal phages, which may have crossed species barriers. Moreover, frequent module exchanges likely occurred exclusively among the subdividing cluster phages. We hypothesize that during evolution, the S. aureus phages enhanced their DNA replication in host cells and the adaptive environment of their host.
Background Plant leaves, as the main photosynthetic organs and the high energy converters among primary producers in terrestrial ecosystems, have attracted significant research attention. Leaf lifespan is an adaptive characteristic formed by plants to obtain the maximum carbon in the long-term adaption process. It determines important functional and structural characteristics exhibited in the environmental adaptation of plants. However, the leaf lifespan and leaf characteristics of urban forests were not studied up to now. Methods By using statistic, linear regression methods and correlation analysis, leaf phenological characters of main tree species in urban forest of Shenyang were observed for five years to obtain the leafing phenology (including leafing start time, end time, and duration), defoliating phenology (including defoliation start time, end time, and duration), and the leaf lifespan of the main tree species. Moreover, the relationships between temperature and leafing phenology, defoliating phenology, and leaf lifespan were analyzed. Findings The timing of leafing differed greatly among species. The early leafing species would have relatively early end of leafing; the longer it took to the end of leafing would have a later time of completed leafing. The timing of defoliation among different species varied significantly, the early defoliation species would have relatively longer duration of defoliation. If the mean temperature rise for 1°C in spring, the time of leafing would experience 5 days earlier in spring. If the mean temperature decline for 1°C, the time of defoliation would experience 3 days delay in autumn. Interpretation There is significant correlation between leaf longevity and the time of leafing and defoliation. According to correlation analysis and regression analysis, there is significant correlation between temperature and leafing and defoliation phenology. Early leafing species would have a longer life span and consequently have advantage on carbon accumulation compared with later defoliation species.
Contents: The Economic Value of Natural Capital and Ecosystem Services / John Box -- Building urban biodiversity through financial incentives, regulation, and targets / John Box -- Delivering urban greenspace for people and wildlife / John Box -- Briefing: Keeping up with the Suds revolution and legislative evolution / Joanne Goodson -- Assessing the Environmental Impact: Are Stormwater Ponds More Effective Than Presumed? / David A Tomasko, Emily H Keenan, Shayne Paynter and Megan Arasteh -- Experimental studies on the effects of nutrient loading and sediment removal on water quality in Lake Hancock / David A Tomasko, Emily C Hyfield Keenan, Loreto C DeBrabandere, Joseph P Montoya and Thomas K Frazer -- Managing Water Quality in Huntsman Lake (Virginia, USA)—Development and Implementation of Restoration Strategies / David Tomasko, Emily Keenan and Shannon Curtis -- Sustaining high nature value farming systems: lessons from the west of Ireland / George F Smith, Paul O’Donoghue and Cliona O’Brien -- Post-industrial and brownfield habitats / Kat Stanhope and John Box -- Translocating wildlife habitats:
a guide for civil engineers / John Box and Kat Stanhope -- Coed Darcy urban village - delivering
biodiversity during redevelopment of a former oil refinery adjacent to a wetland of international importance / J Box, J Nightingale, S Prosser, D McLaughlin, K Perry, M Tooby, C Sellars, K Hills, K Stanhope, J Girgis and P Pech -- How much water do rivers need? Hydroecology and environmental flows / Liam Atherton, Stuart Smith and Brian Cox -- The Olympic Park - A Biodiversity Action Plan in Action / Claire Wansbury and Richard Jackson -- Delivering Wetland Biodiversity in the London 2012 Olympic Park / Ian Morrissey and Mike Vaughan -- Riverfront Landscape Design for London 2012 Olympic Park / Mike McNicholas and Hua Wen -- The Blackwater Valley Road: using green infrastructure for ecological mitigation / Suzanne Glencross, Steve Bailey and Claire Wansbury -- Potential impacts of sea level rise on
Sarasota Bay seagrasses / D.A Tomasko and E.H Keenan -- Otters in Scotland: How Vulnerable
Are They to Disturbance? / Sarah Bassett and Jules Wynn -- Use of badger tunnels by mammals on
Highways Agency schemes in England / Bonnie Eldridge and Jules Wynn -- Habitat Suitability Index Scores as an Indicator of the Presence of Great Crested Newts / Cat Sellars -- Newts prove no bar to operations / Luke Gorman -- Can non-intrusive geo-physical techniques assist in mapping setts of the Eurasian badger? / P O’Donoghue, L Dolan, P D Dansie and I Sharkey -- White-Clawed Crayfish:
Use of Drainage Ditches / Paul O’Donoghue, Ross Macklin and Paul Dansie -- Developing a Grasp of European Eel Conservation / Veronica Lawrie -- Little egret expansion in Ireland: Cork - a case study / Paul O’Donoghue and Patrick Smiddy -- Roman Snail: An Introduction to its Ecology and Legal Protection / Heather Mansfield.
Change in plant phenology is one of the most sensitive ecological responses to climate warming. Little information is known about the effects of climate warming on phenology of urban tree species in the northern forest of China. In this study, we investigated the phenological characteristics of the main tree species in the urban forest of Shengyang City in China and the correlation between phenology and atmospheric temperature from the discontinuous data during past 42 years over three time periods (from 1962 to 1965, 1977 to 1978, and 2000 to 2005). The results showed that the annual average temperature in Shenyang City showed an increasing trend and increased by 0.96°C from 1962 to 2005 due to climate warming. The germination phenology of the urban trees was negatively correlated with the temperature in winter and early spring. The leafing phenology was mainly influenced by the temperature in spring before leafing. Influenced by climate warming, the germination, leafing, and flowering phenologies of this urban forest in 2005 were 14, 13, and 10 days earlier than those in 1962, respectively. We inferred that further warming in winter might prolong the growing season of urban trees in the northern forest of China.
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