Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.

Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus "Nitrosopumilus maritimus" strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.

Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences.

Ribosomal RNA (rRNA) sequences were used to establish the phylogenetic affiliations of symbioses in which prokaryotes appear to confer sulfur-based chemoautotrophy on their invertebrate hosts. Two submarine hydrothermal vent animals, the vestimentiferan tube worm Riftia pachyptila and the clam Calyptogena magnifica, and a tidal-flat bivalve, Solemya velum, were inspected. 5S rRNA's were extracted from symbiont-bearing tissues, separated into unique forms, and their nucleotide sequences determined and related to other 5S rRNA's in a phylogenetic tree analysis. The prokaryotic symbionts are related to one another and affiliated with the same narrow phylogenetic grouping as Escherichia coli and Pseudomonas aeruginosa. The sequence comparisons suggest that Riftia is more closely related to the bivalves than their current taxonomic status would suggest.

Plasmid transfer for enhancing degradation capabilities.

The kinetics of plasmid conjugation for the TOL and RP4 plasmids depend strongly on the donor cells' specific growth rate and substrate concentration, both of which determine the cells' energy availability. Although transfer rates can be large when energy availability is high, normal biological processes have low energy availability. Therefore, we propose and evaluate preliminarily a simple scheme to create a small zone of high energy availability.

Acetivibrio cellulolyticus and Bacteroides cellulosolvens are members of the greater clostridial assemblage.

The nucleotide sequences of the 16S rRNA genes of Acetivibrio cellulolyticus, A. cellulosolvens, and Bacteroides cellulosolvens were determined and shown to be affiliated with the low G + C members of Gram-positive bacteria. The sequences for A. celluolyticus and A. cellulosolvens were revealed to be identical, supporting the proposal by W.D. Murray [Int. J. Syst. Bacteriol. (1986) 36, 314-316] that A. cellulosolvens be correctly classified as A. cellulolyticus. The closest relative to A. cellulolyticus is Clostridium aldrichii, related at 98.5% sequence similarity. B. cellulosolvens and A. cellulolyticus are related at 94.4% sequence similarity.

Comparison of phylogenetic relationships based on phospholipid fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria.

Twenty-five isolates of dissimilatory sulfate-reducing bacteria were clustered based on similarity analysis of their phospholipid ester-linked fatty acids (PLFA). Of these, 22 showed that phylogenetic relationships based on the sequence similarity of their 16S rRNA directly paralleled the PLFA relationships. Desulfobacter latus and Desulfobacter curvatus grouped with the other Desulfobacter spp. by 16S rRNA comparison but not with the PLFA analysis as they contained significantly more monoenoic PLFA than the others. Similarly, Desulfovibrio africanus clustered with the Desulfovibrio spp. by 16S rRNA but not with them when analyzed by PLFA patterns because of higher monoenoic PLFA content. Otherwise, clustering obtained with either analysis was essentially congruent. The relationships defined by PLFA patterns appeared robust to shifts in nutrients and terminal electron acceptors. Additional analyses utilizing the lipopolysaccharide-lipid A hydroxy fatty acid patterns appeared not to shift the relationships based on PLFA significantly except when completely absent, as in Gram-positive bacteria. Phylogenetic relationships between isolates defined by 16S rRNA sequence divergence represent a selection clearly different from the multi-enzyme activities responsible for the PLFA patterns. Determination of bacterial relationships based on different selective pressures for various cellular components provides more clues to evolutionary history leading to a more rational nomenclature.

Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in freshwater sediments.

A protocol was developed for the efficient recovery of intact, high molecular weight rRNA from different environmental matrices. Critical variables were identified in sample processing that influenced yield and integrity of recovered nucleic acid. Most notably, the order of addition and the buffer to sample volume ratio profoundly influenced the efficiency of nucleic acid recovery from sediment material when utilizing a guanidine thiocyanate-beta-mercaptoethaol extraction buffer. Addition of one sample volume to five buffer volumes contributed to an order of magnitude increase in recovery relative to reverse order of addition (buffer addition to sample). An optimized extraction protocol was used to evaluate rRNA yield by seeding samples with whole cells and radiolabeled nucleic acid. Recovery of intact rRNA was confirmed by polyacrylamide gel electrophoresis, which was also used to provide another estimate of quantity. This optimized protocol was used to measure depth-related changes in biomass distribution in Lake Michigan deep-water sediments. This revealed a biomodal biomass distribution; a maximum near the water/sediment interface and a secondary peak associated with the oxic/suboxic boundary. A significant portion of the community at the oxic/suboxic boundary was composed of non-methanogenic Archaea.

Distribution and abundance of Gram-positive bacteria in the environment: development of a group-specific probe.

We developed a 16S rRNA-targeted oligonucleotide probe (S-P-GPos-1200-a-A-13) for the Gram-positive bacteria, confirmed its specificity by database searches and hybridization studies, and investigated the effects of humic acids on membrane hybridizations with this probe. S-P-GPos-1200-a-A-13 was used to estimate the abundance of Gram-positive populations in the bovine rumen and Lake Michigan sediments. This probe should be useful for studies of the environmental distribution of Gram-positive bacteria and the detection of uncultured, phylogenetically Gram-positive bacteria with variable or negative Gram staining reactions, and could serve for Gram staining in some diagnostic settings.

Persistence and functional impact of a microbial inoculant on native microbial community structure, nutrient digestion and fermentation characteristics in a rumen model.

Small sub-unit (SSU) rRNA-targeted oligonucleotide probes were used to monitor the persistence of a genetically engineered bacterium inoculated in model rumens. Eight dual flow continuous culture fermenters were operated with either standard artificial saliva buffer or buffer with chondroitin sulfate (0.5 g/l) added. After 168 h of operation, fermenters were inoculated with Bacteroides thetaiotaomicron BTX (BTX), at approximately 1% of total bacteria. B. thetaiotaomicron was quantified using a species-specific probe and shown to persist in fermenters 144 h after inoculation (relative abundance 0.48% and 1.42% of total SSU rRNA with standard and chondroitin sulfate buffers, respectively). No B. thetaiotaomicron SSU rRNA was detected in fermenter samples prior to inoculation with strain BTX. Relative abundances of Bacteria, Eucarya and Archaea were not affected by either inoculation or buffer type. Fiber digestion, in particular the hemicellulose fraction, increased after strain BTX addition. Chondroitin sulfate addition to the buffer increased bacterial nitrogen flow in fermenters, but did not alter fiber digestion. Neither inoculum nor buffer type altered total short chain fatty acid (VFA) concentrations but proportions of individual VFA differed. In model rumens, B. thetaiotaomicron BTX increased fiber digestion when added to mixed ruminal microbes, independent of chondroitin sulfate addition; but further study is needed to determine effects on other fiber-digesting bacteria.

Implications of the Balanced Budget Act of 1997.

The sweeping and challenging changes in the health care industry emanating from the Balanced Budget Act of 1997 have exceeded those experienced by health care providers and consumers under the Tax Equity and Fiscal Responsibility Act of 1982, the Diagnosis Related Groupings in 1984, and the Resource-Based Relative Value Scale in 1992. To understand and cope with these changes, the financial impact of the Balanced Budget Act is examined in depth, particularly in terms of reimbursement or funding for all health care settings, providers, and medical education. The dramatic changes in the health care delivery process that have caused havoc and turmoil also are examined. For survival and growth under the Balanced Budget Act, reengineering strategies are presented. The ethical and social responsibilities that underlie the current and future impact of the Balanced Budget Act are analyzed to foster the principles of justice, fairness, and best interests of the public.

Business ethics: implications for managed care contracts.

Business ethics is a specialized study that emphasizes how moral standards apply to organizations, policies, procedures and behavior. Moral standards must be considered to understand the implications of business ethics in subacute care.

Capitation, point of service and Medicare select: friends or foes.

Capitation, point of service (POS) and Medicare Select (MedSelect) are significantly influencing today's health care system. Providers need to understand these key market forces and their implications for subacute care.

Ethics in subacute care--Part 2.

When forming ethics committees, a basic understanding of the anatomy of ethics is essential. Part 2 of "Ethics in Subacute Care" applies ethical theories of three major sources of concern in the subacute care environment--organizational, professional practice and managed care contracts.

JCAHO accreditation: a challenge for subacute care providers.

Clearly, subacute care providers who are JCAHO accredited have a competitive edge over those who are not. As Medicare and Medicaid continue to shift to managed care plans and as employers' groups become more familiar with subacute care providers, those that can get accredited within 2 years will be in an excellent position to capture a large share of the market. The challenge, then, is how to prepare for a successful accreditation process.

Disease management: a challenge to subacute care.

Disease management (DM) poses a tremendous challenge to the continued survival and growth of subacute care. Thus, it is imperative that subacute care providers know what DM entails and integrate those protocols being developed, tested and implemented by DM firms and managed care organizations (MCOs).

Balanced Budget Act of 1997: what it means for subacute care.

The Balanced Budget Act of 1997 calls for significant changes in the Medicaid and Medicare programs. Three measures help subacute care providers to meet the changes this act poses: (1) understanding a prospective payment system; (2) developing a financial model; and (3) implementing efficient systems that decrease cost.

Anatomy of a management system.

While a Management System is no panacea for success in managed care, not having such a system can be bazardous to the health of a subacute care facility. The eight components of the Management System and how they relate to subacute care are discussed.

Managing risks in subacute care.

Risk management should improve the quality of care and clinical outcomes as well as prevent litigation. A systematic risk-management program needs objectives, goals, benchmarks and a continuous quality improvement approach. Three basic tenets help: quality, evaluation and utilization management.

Business strategies in subacute care.

To increase market share in a managed care environment, subacute care providers must confront several issues: business strategies, information technology and human resource management. The backbone of the subacute care facility is its human resources, its link to the world is information technology and its foundation is the business plan.

Managed care trends: the effect on subacute care.

Despite the recent mega-mergers of managed care organizations, health maintenance organizations (HMOs) are increasing. To understand what this growth means for subacute providers, trends in HMO enrollment must be identified.