The history of inorganic nitrogen in the biosphere

In quest of the nitrogen oxidizing prokaryotes of the early Earth

The introduction of nitrite and nitrate to the relatively reduced environment of the early Earth provided impetus for a tremendous diversification of microbial pathways. However, little is known about the first organisms to produce these valuable resources. In this review, the latest microbial discoveries are integrated in the evolution of the nitrogen cycle according to the great 'NO-ON' time debate, as we call it. This debate hypothesizes the first oxidation of nitrogen as abiotic and anoxic ('NO') versus biological and aerobic ('ON'). Confronting ancient biogeochemical niches with extant prokaryotic phylogenetics, physiology and morphology, pointed out that the well-described ammonia and nitrite oxidizing Proteobacteria likely did not play a pioneering role in microbial nitrogen oxidation. Instead, we hypothesize ancestral and primordial roles of methanotrophic NC10 bacteria and ammonia oxidizing archaea, respectively, for early nitrite production, and of anammox performing Planctomycetes followed by Nitrospira for early nitrate production. Additional genomic and structural information on the prokaryotic protagonists but also on their phages, together with the continued search for novel key players and processes, should further elucidate nitrogen cycle evolution. Through the ramifications between the biogeochemical cycles, this will improve our understanding on the evolution of terrestrial and perhaps extraterrestrial life.

Purification and properties of a dissimilatory nitrate reductase from Haloferax denitrificans

A membrane-bound nitrate reductase (nitrite:(acceptor) oxidoreductase, EC 1.7.99.4) from the extremely halophilic bacterium Haloferax denitrificans was solubilized by incubating membranes in buffer lacking NaCl and purified by DEAE, hydroxylapatite, and Sepharose 6B gel filtration chromatography. The purified nitrate reductase reduced chlorate and was inhibited by azide and cyanide. Preincubating the enzyme with cyanide increased the extent of inhibition which in turn was intensified when dithionite was present. Although cyanide was a noncompetitive inhibitor with respect to nitrate, nitrate protected against inhibition. The enzyme, as isolated, was composed of two subunits (Mr 116,000 and 60,000) and behaved as a dimer during gel filtration (Mr 380,000). Unlike other halobacterial enzymes, this nitrate reductase was most active, as well as stable, in the absence of salt.

Evolution of bacterial denitrification and denitrifier diversity

Little is known about the role of nitrate in evolution of bacterial energy-generating mechanisms. Denitrifying bacteria are commonly regarded to have evolved from nitrate-respiring bacteria. Some researchers regard denitrification to be the precursor of aerobic respiration; others feel the opposite is true. Currently recognized denitrifying bacteria such as Hyphomicrobium, Paracoccus, Pseudomonas and Thiobacillus form a very diverse group. However, inadequate testing procedures and uncertain taxonomic identification of many isolates may have overstated the number of genera with species capable of denitrification. Nitrate reductases are structurally similar among denitrifying bacteria, but distinct from the enzymes in other nitrate-reducing organisms. Denitryfying bacteria have one of two types of nitrite reductase, either a copper-containing enzyme or an enzyme containing a cytochrome cd moiety. Both types are distinct from other nitrate reductases. Organisms capable of dissimilatory nitrate reduction are widely distributed among eubacterial groups defined by 16S ribosomal RNA phylogeny. Indeed, nitrate reduction is an almost universal property of actinomycetes and enteric organisms. However, denitrification is restricted to genera within the purple photosynthetic group. Denitrification within the genus Pseudomonas is distributed in accordance with DNA and RNA homology complexes. Denitrifiers seem to have evolved from a common ancestor within the purple photosynthetic bacterial group, but not from a nitrate-reducing organism such as those found today. Although denitrification seems to have arisen at the same time as aerobic respiration, the evolutionary relationship between the two cannot be determined at this time.

Nitrogen fixation as evidence for the reducing nature of the early biosphere

Probably the first nitrogen fixers were anaerobic, non-photosynthetic, bacteria, i.e. fermenters. During the evolution of N2 fixation they still needed nitrogen on the oxidation level of ammonia. Because of the complexities in structure and function of nitrogenase this evolution must have required a long time. The photosynthetic and later the respiring bacteria inherited the capacity for N2 fixation from the fermenters, but the process did not change a great deal when it was taken over. Because of the long need for NH3, which is unstable in a redoxneutral atmosphere, a long-persisting reducing atmosphere was needed. The transition to a redoxneutral atmosphere, dominated by CO2, H2O and N2, cannot have been rapid, and the NH3 in it was recycled. Probably the atmosphere contained for a long time, as was suggested by Urey but is often denied now, a great deal of methane as a reductant. The recycling occurred with participation of intermediates like cyanide, through energy input as UV radiation or as electric discharges. A stationary state was set up. The hypothesis is recalled that coloured, photosynthetic, NH3 bacteria, analogous to coloured sulphur bacteria, may have existed, or may still exist, in reducing conditions. A few remarks are made about the origin of nitrification in the later, oxidizing atmosphere.

Evolution of major metabolic innovations in the precambrian

A combination of the information on the metabolic capabilities of prokaryotes with a composite phylogenetic tree depicting an overview of prokaryote evolution based on the sequences of bacterial ferredoxin, 2Fe-2S ferredoxin, 5S ribosomal RNA, and c-type cytochromes shows three zones of major metabolic innovation in the Precambrian. The middle of these, which reflects the genesis of oxygen-releasing photosynthesis and aerobic respiration, links metabolic innovations of the anaerobic stem on the one hand and, on the other, proliferation of aerobic bacteria and the symbiotic associations leading to the eukaryotes. We consider especially those pathways where information on the structure of the enzymes is known. Halobacterium and Thermoplasma (archaebacteria) do not belong to a totally independent line on the basis of the composite tree but branch from the eukaryote cytoplasmic line.

Evolutionary considerations on the thermodynamics of nitrogen fixation

An evolutionary explanation is sought for the fact that ATP is needed for N2 fixation in spite of the exergonicity of the process. After a survey of the state of knowledge about the thermodynamics of N2 fixation in fermenters, photosynthesizers and respirers it is suggested that nitrogenase, which still shows ATP-dependent hydrogenase activity, evolved from an ATP-requiring hydrogenase that lacked nitrogenase activity. The hydrogenase action in the Archaean, reducing, biosphere may have needed ATP to ensure expulsion of H2. Extant non-nitrogenase hydrogenases have lost the dependence on ATP. Because of its complexity, nitrogenase could not rid itself of the ATP dependence or of hydrogenase activity, both wasteful. Presumably all hydrogenases evoled from ferredoxin-like Fe-S proteins.

Antiquity and evolutionary status of bacterial sulfate reduction: sulfur isotope evidence

The presently available sedimentary sulfur isotope record for the Precambrian seems to allow the following conclusions: (1) In the Early Archaean, sedimentary delta 34S patterns attributable to bacteriogenic sulfate reduction are generally absent. In particular, the delta 34S spread observed in the Isua banded iron formation (3.7 x 10(9) yr) is extremely narrow and coincides completely with the respective spreads yielded by contemporaneous rocks of assumed mantle derivation. Incipient minor differentiation of the isotope pattersn notably of Archaean sulfates may be accounted for by photosynthetic sulfur bacteria rather than by sulfate reducers. (2) Isotopic evidence of dissimilatory sulfate reduction is first observed in the upper Archaean of the Aldan Shield, Siberia (approximately 3.0 x 10(9) yr) and in the Michipicoten and Woman River banded iron formations of Canada (2.75 x 10(9) yr). This narrows down the possible time of appearance of sulfate respirers to the interval 2.8--3.1 x 10(9) yr. (3) Various lines of evidence indicate that photosynthesis is older than sulfate respiration, the SO4(2-) Utilized by the first sulfate reducers deriving most probably from oxidation of reduced sulfur compounds by photosynthetic sulfur bacteria. Sulfate respiration must, in turn, have antedated oxygen respiration as O2-respiring multicellular eucaryotes appear late in the Precambrian. (4) With the bulk of sulfate in the Archaean oceans probably produced by photosynthetic sulfur bacteria, the accumulation of SO4(2-) in the ancient seas must have preceded the buildup of appreciable steady state levels of free oxygen. Hence, the occurrence of sulfate evaporites in Archaean sediments does not necessarily provide testimony of oxidation weathering on the ancient continents and, consequently, of the existence of an atmospheric oxygen reservoir.

The position of nitrate respiration in evolution

Egami's hypothesis that oxygen respiration evolved from nitrate respiration, and this from nitrate fermentation, is not accepted. The reasons are: (1) Presumably there was no nitrate before O2 in the biosphere. (2) On mechanistic grounds, respiration (oxidative phosphorylation) is to be derived directly from photosynthesis (photosynthetic phosphorylation) rather than from any form of fermentation.

The length of the transition period from the reducing to the neutral biosphere

The development of the complicated mechanisms for N2 fixation, which in nature is an endergonic process and requires a great deal of ATP, must have taken a long time. During that time primeval NH3 must still, albeit to a decreasing extent, have been available as a source of nitrogen. This is true, whether N2 fixation originally arose in the primitive anaerobes, or, according to Postgate, in more advanced bacteria. As NH3 resists UV radiation only in the presence of excess H2 it follows that the disappearance of H2 and the transition from the reducing to the neutral biosphere also took a long time, probably of the order of 10(9) degrees yr. According to previous evidence, the transition from the neutral to the oxidizing biosphere likewise took long; this length enabled the organisms to adapt the N2 fixing machinery to aerobic conditions.

Two kinds of lithotrophs missing in nature

Two groups of lithotrophic bacteria, the existence of which may be expected on evolutionary and thermodynamical grounds, have not yet been detected: (A) photosynthetic, anaerobic, ammonia bacteria, analogous to coloured sulphur bacteria, and (B) chemosynthetic bacteria that oxidize ammonia to nitrogen with O2 or nitrate as oxidant.

Elemental abundance as a factor in the origins of mineral nutrient requirements

No element is found to be commonly required if it has an abundance of less than about 2 nM in the ocean, 20 mumoles/kg in the earth's crust, or 200 mumoles/100 moles Si in the cosmos. More than 40 elements are above these limits, but only 18 of them are commonly required (6 of these being dispensed with by some organism). It is postulated that all of the required elements fall under one of four hypotheses: H-I--a unique requirement dating from the origin of life; H-II--a unique requirement, acquired later; H-III--a primordial requirement which was satisfied by a number of elements, evolutionary adaptation being made to the most abundant member; H-IV--same as III, but a later acquisition. It is suggested that H, K (vs. Na), Mg (vs. Ca), C, N, O, P, S and Fe fall under H-I. Special requirements such as for B, Se and I fall under H-II. In H-III are K vs. Rb, Mg vs. Be(?), S vs. Se, Clvs. Br, H vs F(?), and Zn and Mn vs. various metals. In H-IV probably fall Ca vs. Sr, Na vs. Li (?), Mo vs. V, and Si vs. Ge. The most abundant heavy metal in the ocean is Zn, which may account for its utilization; other required heavy metals have special utility as electron carriers.